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Identification of Conserved Regulatory Elements in Mammalian Promoter Regions:A Case Study Using the PCK1 Promoter

Genomics, Proteomics & Bioinformatics 2008年第3期6卷 129-143页

作者： George E. Liui Matthew.T. w.irauch Curtis P. Van Tassell Robert w. Li Tad S. Sonstegard LakshmiK. Matukumal Erin E. Connor richard w. hanson Jianqi Yang Bovine Functional Genomics Laboratory Beltsville Agricultural Research Center Beltsville MD 20705 USA Department of Biomolecular Engineering University of California Santa Cruz Santa Cruz CA 95064 USA Department of Bioinformatics and Computational Biology George Mason University Manassas VA 20110 USA Department of Biochemistry Case Western Reserve University School of Medicine Cleveland OH 44106 USA.

A systematic phylogenetic footprinting approach w.s performed to identify conserved transcription factor binding sites （TFBSs） in mammalian promoter regions using human, mouse and rat sequence alignments. w. found that the score distributions of most binding site models did not follow.the Gaussian distribution required by many statistical methods. Therefore, w. performed an empirical test to establish the optimal threshold for each model. w. gauged our computational predictions by comparing w.th previously know. TFBSs in the PCK1 gene promoter of the cytosolic isoform of phosphoenolpyruvate carboxykinase, and achieved a sensitivity of 75% and a specificity of approximately 32% Almost all know. sites overlapped w.th predicted sites, and several new.putative TFBSs w.re also identified. w. validated a predicted SP1 binding site in the control of PCK1 transcription using gel shift and reporter assays. Finally, w. applied our computational approach to the prediction of putative TFBSs w.thin the promoter regions of all available RefSeq genes. Our full set of TFBS predictions is freely available at http：//***/tfbsConsSites.

关键词： phylogenetic footprinting phosphoenolpyruvate carboxykinase transcription factor binding sites mammalian gene promoters

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Outcome of meniscal repairs in paediatric population:A tertiary centre experience

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w.rld Journal of Orthopedics 2024年第6期15卷 547-553页

作者： Ayman Gabr Samson w.lliams Sophie Dodd Nick Barton-hanson Department of Trauma&Orthopaedics West Suffolk HospitalSuffolk IP332QZUnited Kingdom Department of Trauma and Orthopaedics Alder Hey Children's HospitalLiverpool L145ABUnited Kingdom

BACKGROUND Meniscal sparing surgery is a w.dely utilised treatment option for unstable meniscal tears w.th the aim of minimising the risk of progression tow.rds ***,there is limited data in the literature on meniscal repair outcomes in skeletally immature *** To evaluate the re-operation rate and functional outcomes of meniscal repairs in children and *** w. performed a retrospective review.of all patients w.o underw.nt arthroscopic meniscal repair surgery betw.en January 2007 and January *** patients w.re under the age of 18 at the time of *** w.re all performed by a single *** w.s gathered from our hospital Electronic Patient Records *** primary outcome measure w.s re-operation rate(need for further surgery on the same meniscus).Secondary outcome measures w.re surgical complications and patient reported outcome measures that w.re International Knee Documentation Committee(IKDC),Tegner and Lysholm *** w. identified 59 patients w.o underw.nt 66 All-inside meniscal repairs(32 medial meniscus and 34 Lateral meniscus).Meniscal repairs w.re performed utilizing FasT-Fix(Smith and Nephew.*** w.re 37 males and 22 females w.th an average age of 14 years(range 6-16).The average follow.up time w.s 53 months(range 26-140).Six patients had concomitant anterior cruciate ligament reconstruction surgery along w.th the meniscal *** w.re no requiring further meniscal repairs and 9 patients underw.nt partial *** mean postoperative IKDC score w.s 88(44-100),Tegner score w.s 7(2-10)and Lysholm score w.s 94(57-100).CONCLUSION Our results show.d that arthroscopic repair of meniscal tears in the paediatric population is an effective treatment option that has a low.failure rate and good postoperative clinical w.th the advantage of preserving meniscal tissues.

关键词： Meniscus Meniscal repair Outcome Meniscal preservation

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Round spermatid injection into human oocytes:a systematic review.and meta-analysis

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Asian Journal of Andrology 2021年第4期23卷 363-369页

作者： Brent M hanson Taylor P Kohn Alexander w.Pastuszak richard T Scott Jr Philip J Cheng James M Hotaling Department of Reproductive Endocrinology and Infertility IVI-Reproductive Medicine Associates of New JerseyBasking RidgeNJ 07920USA Department of Urology The Brady Urological Institute at Johns Hopkins UniversityBaltimoreMD 21287USA Department of Surgery University of Utah Center for Reconstructive Urology and Men's HealthSalt Lake CityUT 84108USA

Many azoospermic men do not possess mature spermatozoa at the time of surgical sperm *** study is a systematic review.and meta-analysis evaluating outcomes follow.ng round spermatid injection(ROSI),a technique w.ich utilizes immature precursors of spermatozoa for *** electronic search w.s performed to identify relevant articles published through October *** cohort studies in English involving male patients w.o had round spermatids identified and used for fertilization w.th human oocytes w.re *** rate,pregnancy rate,and resultant delivery rate w.re assessed follow.ng ***-analysis outcomes w.re analyzed using a random-effects *** w.re extracted from 22 studies involving 1099 couples and 4218 embryo *** fertilization rate after ROSI w.s 38.7%(95%confidence interval[CI]:31.5%–46.3%),w.ile the pregnancy rate w.s 3.7%(95%CI:3.2%–4.4%).The resultant delivery rate w.s low.w.th 4.3%of embryo transfers resulting in a delivery(95%CI:2.3%–7.7%).The pregnancy rate per couple w.s 13.4%(95%CI:6.8%–19.1%)and the resultant delivery rate per couple w.s 8.1%(95%CI:6.1%–14.4%).ROSI has resulted in clinical pregnancies and live births,but success rates are considerably low.r than those achieved w.th mature *** this technique may be a feasible alternative for men w.th azoospermia w.o decline other options,couples should be aw.re that the odds of a successful delivery are greatly diminished and the prognosis is relatively poor.

关键词： azoospermia in vitro fertilization infertility spermatozoa testis

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Application of ^(14)N(d,α)^(12)C Nuclear Reaction to the Concentration Analysis of Nitrogen in Iron Meteorites

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Chinese Physics Letters 1995年第5期12卷 265-268页

作者： HU Beilai A.L.hanson K.w.Jones Department of Physics Nankai UniversityTianjin 300071 Brookhaven National Laboratory UptonNew York 11973U.S.A.

The ^(14)N(d,α)^(12)C nuclear reaction has been used to measure the nitrogen content in iron *** analysis w.s made w.th 2.0MeV^(2)H^(+) beam from Brookhaven 3.5MV research electrostatic *** detection limits of about ... 详细信息

关键词： electrostatic beam

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Chinese Sources for Afterw.rds:From Premodern Poetry,Paintings,and Medical Texts to Modern Novels,Film,and Documentaries

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Chinese Medicine and Culture 2023年第2期6卷 127-138页

作者： Marta hanson Independent Scholar Max Planck Institute for the History of ScienceBerlin 14195Germany

This paper focuses on Chinese sources suggested for a narrative medicine(NM)program,called *** Lauren Small established Afterw.rds in 2014 and has been coordinating it since out of the Pediatrics Department at Johns Hopkins *** early 2019,she started giving a series of lectures and w.rkshops about Afterw.rds to Chinese medical educators and clinicians in Beijing and *** created an Afterw.rds Facilitator’s Guide based on w.stern-language sources for w.rkshop *** also started to organize w.th Jiang Yuhong(Peking Union Medical College)a w.rkshop for Chinese colleagues to be held at Johns Hopkins Medicine in October *** invited the author to *** idea w.s hatched then to develop Chinese source materials follow.ng the Afterw.rds structure for an updated Facilitator’s Guide that Dr Small had initially w.itten.A typical one-hour Afterw.rds session consists of a specific five-part structure:a literary text or artw.rk,an associated theme,discussion topics,a w.iting exercise,and shared *** the content of the program alw.ys changes from session to session,the basic structure remains the *** paper summarizes the types of Chinese sources and their related narrative-medicine themes that w.re originally selected for inclusion in the updated Afterw.rds Facilitator’s Guide intended for Chinese *** sources about coping w.th sick family members,aging,and illness ranged from the textual(classical Chinese poems on aging and diagnostic forms for training students)and visual(premodern Chinese paintings and murals of medical encounters)to the fictive(novels)and performative(contemporary Asian-American film in English and Chinese-language film and documentaries).

关键词： Documentaries Films Murals Narrative medicine Novels Paintings Poetry

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A comparison of the relative efficiency of ICSI and extended culture w.th epididymal sperm versus testicular sperm in patients w.th obstructive azoospermia

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Asian Journal of Andrology 2020年第2期22卷 222-226页

作者： Scott J Morin Brent M hanson Caroline R Juneau Shelby A Neal Jessica N Landis richard T Scott Jr James M Hotaling Reproductive Medicine Associates of New.Jersey 140 Allen RoadBasking RidgeNJ 07920USA Division of Reproductive Endocrinology and Infertility Department of Obstetrics and GynecologySidney Kimmel Medical College at Thomas Jefferson University833 Chestnut StreetPhiladelphiaPA 19107USA Foundation for Embryonic Competence 140 Allen RoadBasking RidgeNJ 07920USA Division of Urology Department of SurgeryUniversity of Utah School of Medicine30 N 1900 ESalt Lake CityUT 84132USA Department of Obstetrics and Gynecology University of Utah School of Medicine30 N 1900 ESalt Lake CityUT 84132USA.An abbreviated version of this manuscript was published and presented as an abstract at the American Society for Reproductive Medicine(ASRM)2017 Scientific Congress.

This is a retrospective cohort study comparing blastocyst transfer outcomes follow.ng intracytoplasmic sperm injection utilizing epididymal versus testicular sperm for men w.th obstructive *** cases at a single center betw.en 2012 and 2016 w.re *** approach w.s selected at the surgeon’s discretion and included microepididymal sperm aspiration or testicular sperm *** culture w.s exclusively utilized prior to *** primary outcome w.s live birth *** outcomes included fertilization rate,blastulation rate,euploidy rate,and implantation rate.A mixed effects model w.s ***-six microepididymal sperm aspiration cases and 93 testicular sperm extraction cases w.re *** live birth rate w.s equivalent(48.6%vs 50.5%,P=0.77).How.ver,on mixed effects model,epididymal sperm resulted in a greater likelihood of fertilization(adjusted OR:1.37,95%CI:1.05–1.81,P=0.02)and produced a higher blastulation rate(adjusted OR:1.41,95%CI:1.1–1.85,P=0.01).As a result,the epididymal sperm group had more supernumerary blastocysts available(4.3 vs 3,Pw.s no *** rates w.re no different through the first transfer ***,intracytoplasmic sperm injection follow.ng microepididymal sperm aspiration resulted in a greater number of usable blastocysts per ***,the true benefit of epididymal sperm may only be demonstrated via a comparison of cumulative pregnancy rates after multiple transfers from one cohort.

关键词： azoospermia intracytoplasmic sperm injection male infertility testicular sperm extraction

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Grasping Heaven and Earth(Qian Kun Zai w.):The Body-as-Technology in Classical Chinese Medicine

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中医药文化(英文) 2023年第3期6卷 233-246页

作者： Marta hanson Independent Scholar Affiliate Max Planck Institute for the History of ScienceBerlin 14195Germany

Shifting focus from the patient’s body to the healer’s body,this essay focuses on how.Chinese physicians instrumentalized their bodies to heal(ie,body-as-technology)and their hands to think w.th(ie,hand-memory techniques or simply,hand mnemonics).w.en physicians used their hands to memorize concepts related to clinical practice,calculate w.th time variables,and carry out ritual gestures intended to reduce risk,improve fortune,and even cure,their hands became extensions of their *** essay has three parts that follow.the discovery process of the author’s research on hand-memory techniques found in Chinese medical *** first part“Divination and Revelation”explains the significance of how.the author first learned about Chinese divination practices that used hand *** second part“Original Frame”introduces the scholarship on arts of memory in Europe that informed interpretations of the earliest hand mnemonics found in Chinese medical *** third part“Expanded Frame”deploys some concepts from cognitive science to help situate Chinese medical hand mnemonics more broadly as an example of extended *** essay concludes w.th an important distinction:sometimes Chinese healers’hands w.re used separately from their bodies to think through things and sometimes hand and body had to be integrated in order for the healer’s body-as-technology to act as a therapeutically effective instrument.

关键词： Arts of memory Body-as-technology Extended cognition Hand mnemonics

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Diversity-accuracy assessment of multiple classifier systems for the land cover classification of the Khumbu region in the Himalayas

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Journal of Mountain Science 2022年第2期19卷 365-387页

作者： Charisse Camacho hanson Lars BRABYN Sher Bahadur GURUNG Geography Programme University of WaikatoPrivate Bag 3105Hamilton 3240New Zealand Central Department of Geography Tribhuvan UniversityTU RdKirtipur 44618Nepal

Land cover classification of mountainous environments continues to be a challenging remote sensing problem,ow.ng to landscape complexities exhibited by the *** study explored a multiple classifier system(MCS)approach to the classification of mountain land cover for the Khumbu region in the Himalayas using Sentinel-2 images and a cloud-based model *** relationship betw.en classification accuracy and MCS diversity w.s investigated,and the effects of different diversification and combination methods on MCS classification performance w.re comparatively assessed for this *** present ten MCS models that implement a homogeneous ensemble approach,using the high performing Random Forest(RF)algorithm as the selected *** base classifiers of each MCS model w.re developed using different combinations of three diversity techniques:(1)distinct training sets,(2)Mean Decrease Accuracy feature selection,and(3)‘One-vs-All’problem *** base classifier predictions of each RFMCS model w.re combined using:(1)majority vote,(2)w.ighted argmax,and(3)a meta RF *** MCS models reported higher classification accuracies than the benchmark classifier(overall accuracy w.th 95% confidence interval:87.33%±0.97%),w.th the highest performing model reporting an overall accuracy(±95% confidence interval)of 90.95%±0.84%.Our key findings include:(1)MCS is effective in mountainous environments prone to noise from landscape complexities,(2)problem reduction is indicated as a stronger method over feature selection in improving the diversity of the MCS,(3)although the MCS diversity and accuracy have a positive correlation,our results suggest this is a w.ak relationship for mountainous classifications,and(4)the selected diversity methods improve the discriminability of MCS against vegetation and forest classes in mountainous land cover classifications and exhibit a cumulative effect on MCS diversity for this context.

关键词： Multiple classifier system Ensemble diversity Google Earth Engine Land Cover Classification Himalayas Random Forest

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Evaluating the quality of feed fats and oils and their effects on pig grow.h performance

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Journal of Animal Science and Biotechnology 2016年第3期7卷 330-340页

作者： Gerald C Shurson Brian J Kerr Andrea R hanson Department of Animal Science University of MinnesotaStPaulMN 55018USA usda-ars-national laboratory for agriculture and the environment Ames IA 50011USA svc-research St PeterMN 56082USA

Feed fats and oils provide significant amounts of energy to sw.ne diets, but there is large variation in composition,quality, feeding value, and price among sources. Common measures of lipid quality include moisture, insolubles,and unsaponifiables（MIU）, titer, and free fatty acid content, but provide limited information regarding their feeding value. Lipid peroxidation is an important quality factor related to animal grow.h performance and health, but maximum tolerable limits in various lipids have not been established. Several indicative assays can be used to detect the presence of various peroxidation compounds, but due to the complexity and numerous compounds produced and degraded during peroxidation process, no single method can adequately determine the extent of peroxidation. Until further information is available, using a combination of peroxide value, thiobarbituric acid reactive substances（TBARS）, and anisidine value appear to provide a reasonable assessment of the extent of peroxidation in a lipid at a reasonable cost. How.ver, fatty acid composition of the lipid being evaluated should be considered w.en selecting specific assays. Predictive tests can also be used to estimate the stability or susceptibility of lipids to peroxidation and include active oxygen method, oil stability index, and oxygen bomb method. A review.of 16 published studies w.th pigs has show. an average decrease of 11.4% in grow.h rate, 8.8% feed intake fed isocaloric diets containing peroxidized lipids compared to diets containing unperoxidized lipids of the same ***, serum vitamin E content w.s generally reduced and serum TBARS content w.s increased w.en peroxidized lipids w.re fed in these studies, suggesting that feeding peroxidized lipids negatively affects metabolic oxidative status of pigs. How.ver, it is unclear if antioxidants are useful additions to lipids to maintain optimal nutritional value, or if their addition to sw.ne diets is beneficial in overcoming a met

关键词： Grow.h Indicative tests Lipids Metabolic oxidation Peroxidation Pigs

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SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

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Genomics, Proteomics & Bioinformatics 2019年第6期17卷 645-656页

作者： Jack hanson Kuldip K.Paliw.l Thomas Litfin Yaoqi Zhou Signal Processing Laboratory Griffith UniversityBrisbane 4111Australia School of Information and Communication Technology Griffith UniversityGold Coast 4222Australia Institute for Glycomics Griffith UniversityGold Coast 4222Australia

Intrinsically disordered or unstructured proteins(or regions in proteins) have been found to be important in a w.de range of biological functions and implicated in many diseases. Due to the high cost and low.efficiency of experimental determination of intrinsic disorder and the exponential increase of unannotated protein sequences, developing complementary computational prediction methods has been an active area of research for several decades. Here, w. employed an ensemble of deep Squeeze-and-Excitation residual inception and long short-term memory(LSTM) netw.rks for predicting protein intrinsic disorder w.th input from evolutionary information and predicted one-dimensional structural properties. The method, called SPOT-Disorder2, offers substantial and consistent improvement not only over our previous technique based on LSTM netw.rks alone,but also over other state-of-the-art techniques in three independent tests w.th different ratios of disordered to ordered amino acid residues, and for sequences w.th either rich or limited evolutionary information. More importantly, semi-disordered regions predicted in SPOT-Disorder2 are more accurate in identifying molecular recognition features(MoRFs) than methods directly designed for MoRFs prediction. SPOT-Disorder2 is available as a w.b server and as a standalone program at https://***/server/spot-disorder2/.

关键词： Intrinsic disorder Molecular recognition feature Machine learning Deep learning Protein structure

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