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APIR: Aggregating Universal Proteomics Datab.se Search Algorithms for Peptide Identification with FDR Control

GENOMICS PROTEOMICS & b.OINFORMATICS 2024年第2期22卷 qzae042页

作者： Chen, Yiling Elaine Ge, Xinzhou Woyshner, Kyla McDermott, Meilu Manousopoulou, Antigoni Ficarro, Scott b. Marto, Jarrod A. Li, Kexin Wang, Leo David Li, Jingyi Jessica Univ Calif Los Angeles Dept Stat & Data Sci Los Angeles CA 90095 USA Univ Calif Los Angeles Bioinformat Interdept Program Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Computat Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biostat Los Angeles CA 90095 USA City Hope Natl Med Ctr Beckman Res Inst Dept Immuno Oncol Duarte CA 91010 USA Univ Southern Calif Dept Quantitat & Computat Biol Los Angeles CA 90007 USA City Hope Natl Med Ctr Dept Pediat Duarte CA 91010 USA b.igham & Womens Hosp Dept Canc Biol Boston MA 02215 USA b.igham & Womens Hosp Dana Farber Canc Inst Blais Prote Ctr Dept Pathol Boston MA 02215 USA Harvard Med Sch Boston MA 02215 USA

Advances in mass spectrometry (MS) have enab.ed high-throughput analysis of proteomes in b.ological systems. The state-of-the-art MS data analysis relies on datab.se search algorithms to quantify proteins b. identifying peptide-spectrum matches (PSMs), which convert mass spectra to peptide sequences. Different datab.se search algorithms use distinct search strategies and thus may identify unique PSMs. However, no existing approaches can aggregate all user-specified datab.se search algorithms with a guaranteed increase in the numb.r of identified peptides and a control on the false discovery rate (FDR). To fill in this gap, we proposed a statistical framework, Aggregation of Peptide Identification Results (APIR), that is universally compatib.e with all datab.se search algorithms. Notab.y, under an FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual datab.se search algorithms do. Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual datab.se search algorithms and empirically controls the FDR. Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed b. some individual datab.se search algorithms. The APIR framework is easily extendab.e to aggregating discoveries made b. multiple algorithms in other high-throughput b.omedical data analysis, e.g., differential gene expression analysis on RNA sequencing data. The APIR R package is availab.e at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide-spectrum match Peptide identification Aggregation of lists FDR control PROTEIN IDENTIFICATION b.CA2 MUTATIONS CELL-CYCLE TANDEM TARGET CANCER PREVALENCE EXPRESSION GENE APOPTOSIS

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Natural Silicate as a Solid Support for the Calix[4]Thiophosphorus Derivative for Removal Mercury (II), as Picrate from Water

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Advances in Chemical Engineering and Science 2024年第2期14卷 74-83页

作者： Walther b. Aparicio-Aragon Tania Deza-Ramos School of Chemical Engineering Chemical Engineering Department Altiplano National University Puno Per&#250

Currently a technique widely used for gold extraction is mercury b. amalgamation technique, the tailing produced pollutes water of all kinds, so it is necessary to develop a form of selective mitigation, for which it is necessary to use complexing agents b.sed on calixarene functionalized with mercury sequestering agents. These are immob.lized b. adding supports b.sed on natural silica to form polymers and make them insolub.e in all types of solvents, so that they can b. used as an extractor and at the same time regenerate to their original properties for continuous reuse.

关键词： Extraction Amalgamation Polymer Natural Silicate Calixarene

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Need for operational simplicity and timely disb.rsal of b.nefits—a qualitative exploration of the implementation of a direct b.nefit transfer scheme for persons with tub.rculosis in India

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贫困所致传染病(英文) 2024年第3期13卷 58-72页

作者： Mohan Malu Thangaraj Jeromie W. V. Pandey Sumit Priya G. Sri Lakshmi Arunachalam Sivavallinathan Sharma Rahul Shewade Hemant Deepak Aishwarya b. Afeeq K. Khatoon Afsana Gokulvijay b. Sireesha Gude Chandra Kavita Nandhakumar S. Samuel Prince Viswanathan C. Nanditha Shanmugasundaram Devika Rao Raghuram Murhekar Manoj V. Jeyashree Kathiresan Indian Council of Medical Research-National Institute of Epidemiology R-127 TNHB Ayapakkam Chennai Tamil Nadu India Tb.Support Network WHO Country Office for India New Delhi India Central Tub.rculosis Division Government of India New Delhi India

b.ckground Ni-kshay Poshan Yojana (NPY) is a direct b.nefit transfer scheme of the Government of India introduced in 2018 to support the additional nutritional requirements of persons with Tb.(PwTb.. Our recent nationwide evaluation of implementation and utilization of NPY using programmatic data of PwTb.from nine randomly selected Indian states, reported a 70% coverage and high median delay in b.nefit credit. We undertook a qualitative study b.tween January and July 2023, to understand the detailed implementation process of NPY and explore the enab.ers and b.rriers to effective implementation and utilization of the NPY *** We followed a grounded theory approach to inductively develop theoretical explanations for social phenomena through data generated from multiple sources. We conducted 36 in-depth interviews of national, district and field-level staff of the National Tub.rculosis Elimination Programme (NTEP) and NPY b.neficiaries from 30 districts across nine states of India, selected using theoretical sampling. An analytical framework developed through inductive coding of a set of six interviews, guided the coding of the sub.equent interviews. Categories and themes emerged through constant comparison and the data collection continued until theoretical *** Stakeholders perceived NPY as a b.neficial initiative. Strong political commitment from the state administration, mainstreaming of NTEP work with the district pub.ic healthcare delivery system, availab.lity of good geographic and internet connectivity and state-specific grievance redressal mechanisms and innovations were identified as enab.ers of implementation. However, the complex, multi-level b.nefit approval process, difficulties in accessing b.nking services, perceived inadequacy of b.nefits and overworked human resources in the NTEP were identified as b.rriers to implementation and *** The optimal utilization of NPY is enab.ed b. strong political commitment and

关键词： National Tub.rculosis Elimination Programme Nutritional status Direct b.nefit transfer Ni-kshay Poshan Yojana Implementation Cash transfer scheme Grounded theory India

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Gas Exchange Rates of Texas Persimmon (Diospyros texana) in Central Texas Woodlands

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American Journal of Plant Sciences 2024年第5期15卷 329-348页

作者： Matthew b. Grunstra Oscar W. Van Auken Department of Integrative b.ology University of Texas at San Antonio San Antonio TX USA

Diospyros texana (Texas persimmon) is a secondary species in most Juniperus ashei/Quercus fusiformis woodlands in central Texas. It has high density, b.t plants are mostly in the community understory. Light response curves at amb.ent and elevated levels of COb.2b. and temperature were measured for D. texana. The Ab.netb. (photosynthetic rate) increased significantly as b.th light level and COb.2b. levels increased b.t not temperature. The Ab.maxb. (maximum photosynthetic rate) of D. texana in full sun at elevated levels of COb.2b. was increased for all treatments. Stomatal conductance increased with levels of COb.2b. b.t only if the interaction was removed from the model. Intercellular levels of COb.2b. increased with b.th temperature and COb.2b. treatments as did water use efficiency (WUE). Furthermore, light saturation (Lb.satb.) increased with COb.2b. treatments and light compensation (Lb.cpb.) increased with temperature. The dark respiration (Rb.db.) increased with b.th temperature and COb.2b. treatments. Markov population models suggested D. texana populations would remain ecologically similar in the future. However, sub.canopy light levels and herb.vory should b. considered when examining population projections. For example, Juniperus ashei juveniles are not recruited into any canopy unless there are high light levels. Herb.vory reduces the success of Quercus juveniles from reaching the canopy. These factors do not seem to b. a prob.em for D. texana juveniles which would allow them to reach the canopy without need of a high light gap and are not prevented b. herb.vory. Thus, Juniperus/Quercus woodlands will change in the future to woodlands with D. texana a more common species.

关键词： Replacement Dynamics Ecological Succession CO2 Concentrations Temperature Levels Photosynthetic Rates Drought Tolerance Herb.vory Species Replacement Encroachment Juniper

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Long-term olfactory loss post-COVID-19:Pathob.ology and potential therapeutic strategies

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World Journal of Otorhinolaryngology-Head and Neck Surgery 2024年第2期10卷 148-155页

作者： Sarah Kim John b.Finlay Tiffany Ko b.adley J.Goldstein Department of Head and Neck Surgery&Communication Sciences Duke UniversityDurhamNorth CarolinaUSA Medical Scientist Training Program Duke UniversityDurhamNorth CarolinaUSA Department of Neurob.ology Duke UniversityDurhamNorth CarolinaUSA

An acute loss of smell emerged as a striking symptom present in roughly half of the people infected with the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)virus in the early phases of the COVID-19 *** most COVID-19 patients,olfaction recovers over the course of a few ***,a lasting partial or complete loss of smell,often associated with distorted olfactory perceptions termed parosmia,has emerged as a widespread prob.em impacting at least 5%-10%of those who experience anosmia due to *** inab.lity to offer effective therapies to this hyposmic or anosmic population,comprising millions of patients,highlights an enormous unmet need for the medical ***,we summarize the current understanding of the pathob.ology causing acute olfactory loss due to SARS-CoV-2 infection,focusing on how the virus interacts with the peripheral olfactory system,a major site of viral *** also explore the prob.em of long-COVID olfactory dysfunction,which may accompany other persistent systemic disorders collectively termed postacute sequelae of ***,we discuss an emerging model focused on unresolved immune cell activity driving ongoing ***,we review current and future therapeutic approaches aimed at restoring olfactory function.

关键词： hyposmia inflammation long-COVID parosmia

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Effect of drug therapies on self-reported chemosensory outcomes after COVID-19

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World Journal of Otorhinolaryngology-Head and Neck Surgery 2024年第2期10卷 88-96页

作者： Marco A.Fornazieri b.uno M.Cunha Samuel P.Nicácio Lucas K.Anzolin JoséL.b.da Silva Aristides Fernandes Neto Deusdedit b.andão Neto richard L.Voegels Fáb.o D.R.Pinna Department of Surgery Londrina State UniversityLondrinaBrazil Department of Medicine Pontifical Catholic University of ParanáLondrinaBrazil Department of Otorhinolaryngology University of São PauloSao PauloBrazil Department of Otorhinolaryngology:Head and Neck Surgery Perelman School of MedicineSmell and Taste CenterUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA

Ob.ective:The aim of this study was to assess the relative efficacy of medications used following severe acute respiratory syndrome coronavirus-2(SARS-CoV-2)infection on self-reported alterations in taste and/or smell ***:Seven hundred and fourteen persons with self-reported postcoronavirus disease 2019(post-COVID-19)chemosensory disorders were personally interviewed regarding specific medications they were administered following the acute phase of the *** dependent measure—self-reported total recovery of chemosensory symptoms—was sub.ected to stepwise logistic *** predictors included demographic and clinical variab.es,in addition to specific medications used to mitigate disease symptoms(i.e.,systemic corticosteroids,oseltamivir,vitamin C,ib.profen,hydroxychloroquine,azithromycin,ivermectin,nitazoxanide,anticoagulants,and zinc).Results:The median time b.tween COVID-19 symptom onset and the interviews was 81 days(interquartile range:60-104).Of the 714 sub.ects,249(34.9%)reported total recovery of their chemosensory function;437(61.2%)had at least one treatment since the b.ginning of the *** and those with more comorb.dities had undergone more *** recovery rates of the treated and nontreated groups did not differ ***,respondents who had used nitazoxanide tended to have a higher rate of self-reported taste or smell *** who took oral zinc were less likely to ***:No medication employed during the first months after SARS-CoV-2 infection had a clear positive effect on returning self-reported smell or taste function to normal,although nitrazoxide trended in a positive *** zinc had a negative effect on the reported recovery of these senses.

关键词： chemosensory disorder coronavirus infections COVID-19 drug therapy SARS-CoV-2 smell loss taste loss

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A Modified Lagrange Method for Solving Convex Quadratic Optimization Prob.ems

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Open Journal of Optimization 2024年第1期13卷 1-20页

作者： Twum b. Stephen Avoka John Christian J. Etwire School of Mathematical Science C. K. Tedam University of Technology and Applied Sciences Navrongo Ghana Department of Mathematics University for Development Studies Tamale Ghana

In this paper, a modified version of the Classical Lagrange Multiplier method is developed for convex quadratic optimization prob.ems. The method, which is evolved from the first order derivative test for optimality of the Lagrangian function with respect to the primary variab.es of the prob.em, decomposes the solution process into two independent ones, in which the primary variab.es are solved for independently, and then the secondary variab.es, which are the Lagrange multipliers, are solved for, afterward. This is an innovation that leads to solving independently two simpler systems of equations involving the primary variab.es only, on one hand, and the secondary ones on the other. Solutions ob.ained for small sized prob.ems (as preliminary test of the method) demonstrate that the new method is generally effective in producing the required solutions.

关键词： Quadratic Programming Lagrangian Function Lagrange Multipliers Optimality Conditions Sub.idiary Equations Modified Lagrange Method

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The Sigma-1 Receptor as a Pharmacologic Chaperone: Energetics

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Journal of b.osciences and Medicines 2024年第8期12卷 347-356页

作者： Rob.rt b. Raffa Joseph V. Pergolizzi Jr. School of Pharmacy (Emeritus) Temple University Philadelphia PA USA College of Pharmacy (Adjunct) University of Arizona Tucson AZ USA NEMA Research Naples FL USA

Initially thought to b. an opioid receptor sub.ype, Sigma-1 receptors (S1R) are now known to b. unique proteins that have chaperone-like properties. As such, they play critical roles in cellular signaling, homeostasis, and cell survival. These roles offer significant insight for understanding homeostasis of normal physiologic processes, and the pathophysiologic consequences of disruption of normal function. b.cause of the b.oad nature of chaperone action, S1R agonists and antagonists represent potential drug discovery goals for the pharmacotherapeutic treatment of a variety of disorders that result from dysfunctional proteins. The present study summarizes the S1R as a pharmacologic chaperone crucial for protein folding and cellular homeostasis. Through literature review and thermodynamic analysis, it explores how S1R stab.lizes target proteins, influencing neuroprotection and potential drug therapies. The b.nding of chaperones to target proteins is thermodynamically favorab.e, offering insights into treating diseases linked to protein misfolding.

关键词： Chaperone Sigma-1 Receptor Energetics Thermodynamics Isothermal Titration Microcalorimetry

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The Impacts and Causes of Land Fragmentation on Farm Productivity: Case Review of East African Countries

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Open Journal of Ecology 2024年第5期14卷 455-482页

作者： Joseph Mayindo Mayele Jacob.b. Kolleh Joel Emmanuel Sab.ri Department of Agricultural and Resource Economics The University of Tokyo Tokyo Japan Department of Forestry and Wildlife College of Natural Resources and Environmental Studies University of Juba Juba South Sudan Department of Socio-Economic and Applied Statistics Central Agricultural Research Institute (CARI) Suakoko Liberia

This report provides an overall assessment of land fragmentation prob.ems in East Africa. Many parts of East Africa have b.come highly fragmented, putting development systems and activities in these areas at risk of complete collapse. Land fragmentation occurs when land gets converted for agriculture, industrialization, or urb.nization, invaded b. non-local plants, or enclosed for individual use and b. sub.ividing farmlands into sub.equent smaller units called parcels with varying average farm sizes. Fragmentation results from inappropriate agricultural development processes and ineffective land use planning that fails to recognize how farmland is used, and the importance of its interconnected areas. Insecurity of tenure and resource rights are key factors in making this possib.e. Land fragmentation is one of the key reasons why the ab.lity of most resources in East Africa b.comes scarcer, and those remaining b.come “privatized” b. more powerful community memb.rs—keen to maintain their access to them. Such individualistic attitudes are new and disadvantage the poorest even further b. affecting the traditional customary safety nets and agricultural outputs. Neither the government nor customary governance systems effectively protect resource access for the poorest. This review summary report identifies the key causes, measures, and implications, government interventions, and the common remedies to land fragmentation prob.ems in the East African Countries of Kenya, Uganda, Rwanda, and Tanzania including neighb.ring Ethiopia, and the Sudan. The findings indicated from 2005 to 2015, the population kept increasing for all the named countries in East Africa with Rwanda and Uganda having a sub.tantial increase in population density. The study review further explores the trend in the performance of agriculture b. average farm sizes within the intervals of five years b. highlighting their strong linkages and found that the average farm size has declined drastically, especiall

关键词： Land Fragmentation Land Consolidation Farm Productivity Industrialization Impacts Causes Average Farm Size Population East Africa

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Rare earth-doped mixed Ni-Cu-Zn ferrites as an effective photocatalytic agent for active degradation of Rhodamine b.dye

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Journal of Rare Earths 2024年第3期42卷 488-496,I0003页

作者： Swapnil A.Jadhav Sandeep b.Somvanshi Sudarshan S.Gawali Kranti Zakde K.M.Jadhav Department of Physics Dr.Babasaheb Ambedkar Marathwada UniversityAurangabad431004MaharashtraIndia School of Materials Engineering Purdue UniversityWest Lafayette 47906USA University Department of b.sic and Applied Sciences MGM UniversityAurangabad431003MaharashtraIndia

In this study, a series of Gd^(3+)-doped mixed Ni-Cu-Zn ferrites with composition of Zn_(0.5)Ni_(0.3)Cu_(0.2)Fe_(2-x)Gd_(x)O_(4)(x = 0, 0.025, 0.05, 0.075, 0.1) was prepared using self-ignition sol-gel method. The prepared nanoparticles with an average size ranging from 22 to 26 nm show a single-phase cub.c structure b.longing to the spinel matrix. A rise in the Gd^(3+)concentration leads to an increase in crystallite size and lattice parameter. In Fourier transform infrared spectra, two main ab.orption b.nds b.longing to the spinel structure are ob.erved. The high-frequency b.nds(v_(1)) represent the tetrahedral complex, while the lowfrequency b.nds(v_(2)) signify the octahedral complex. The optical b.ndgap of the nanoferrites is found within the range of 2.91 to 2.41 eV, depending on their size. The magnetic characteristics of the material,such as saturation magnetization and coercivity are significantly altered with the concentration of Gd^(3+)in the solution. Using Rhodamine b.Rhb. as a model organic pollutant, an in-depth investigation of the photocatalytic activity of the compounds was carried out. The present outcomes show that adding an adequate amount of Gd^(3+)significantly enhances the numb.r of hydroxyl radicals produced b. the ferrite,in turn, increasing the photocatalytic activity of the material. Mechanism elucidated b. scavenger studies reveals that ·OH and holes are the primary reactive radicals responsib.e for the degradation *** photocatalysts show an insignificant performance loss in five consecutive cycles. Thus, it is concluded that these photocatalysts are highly suitab.e for the remediation of dye-contaminated wastewater.

关键词： Gd^(3+)sub.titution Spinel ferrite Structural properties Magnetic properties Photocatalysis Rare earths

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