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Modeling Bacterial species: Using sequence similarity with Clustering Techniques

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Computers, Materials & Continua 2021年第8期68卷 1661-1672页

作者： Miguel-Angel sicilia Elena García-Barriocanal Marçal Mora-Cantallops salvador sánchez-alonso Lino González University of Alcalá Alcaláde Henares(Madrid)28871Spain Camilo JoséCela University Madrid28007Spain

Existing studies have challenged the current definition of named bacterial species,especially in the case of highly recombinogenic bacteria.This has led to considering the use of computational procedures to examine potential bacterial clusters that are not identified by species naming.This paper describes the use of sequence data obtained from MLsT databases as input for a k-means algorithm extended to deal with housekeeping gene sequences as a metric of similarity for the clustering process.An implementation of the k-means algorithm has been developed based on an existing source code implementation,and it has been evaluated against MLsT data.Results point out to potential bacterial clusters that are close to more than one different named species and thus may become candidates for alternative classifications accounting for genotypic information.The use of hierarchical clustering with sequence comparison as similarity metric has the potential to find clusters different from named species by using a more informed cluster formation strategy than a conventional nominal variant of the algorithm.

关键词： Clustering bacterial species k-means sequence alignment

Diagnosis and treatment of hepatocellular carcinoma: An update

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World Journal of Hepatology 2015年第3期7卷 362-376页

作者： Javier Tejeda-Maldonado Ignacio García-Juárez Jonathan Aguirre-Valadez Adrián González-Aguirre Mario Vilatobá-Chapa Alejandra Armengol-alonso Francisco Escobar-Penagos Aldo Torre Juan Francisco sánchez-ávila Diego Luis Carrillo-Pérez Department of Internal Medicine Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Department of Gastroenterology Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Department of Interventional Radiology Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Department of Transplantation Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Department of Hematology and Oncology Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán

Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population; in cirrhotic patients, it is the primary cause of death. The diagnosis is usually delayed in spite of at-risk population screening recommendations, i.e., patients infected with hepatitis B or C virus. Hepatocarcinogenesis hinges on a great number of genetic and molecular abnormalities that lead to tumor angiogenesis and foster their dissemination potential. The diagnosis is mainly based on imaging studies such as computed tomography and magnetic resonance, in which lesions present a characteristic classical pattern of early arterial enhancement followed by contrast medium "washout" in late venous phase. On occasion, when imaging studies are not conclusive, biopsy of the lesion must be performed to establish the diagnosis. The Barcelona Clinic Liver Cancer staging method is the most frequently used worldwide and recommended by the international guidelines of HCC management. Currently available treatments include tumor resection, liver transplant, sorafenib and locoregional therapies(alcoholization, radiofrequency ablation, chemoembolization). The prognosis of hepatocarcinoma is determined according to the lesion's stage and in cirrhotic patients, on residual liver function. Curative treatments, such as liver transplant, are sought in patients diagnosed in early stages; patients in more advanced stages, were not greatly benefitted by chemotherapy in terms of survival until the advent of target molecules such as sorafenib.

关键词： Hepatocellular carcinoma surveillance Liver transplant sorafenib Catheter ablation

Affective and Behavioural Dysfunctions in Patients with subcortical stroke

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Neuroscience & Medicine 2012年第2期3卷 141-148页

作者： Luis Gutierrez Cabello Isabel Gómez-Ruiz Angel Aguilar alonso salvador Pedraza Gutiérrez (IDI) service of Radiology Dr Josep Trueta University Hospi-tal Girona Spain Department of Basic Psychology University of Barcelona Barcelona Spain Department of Neurology Hospital General de L’Hospitalet Hospitalet de Llobregat University of Barcelona Barcelona Spain Department of Personality Psychological As-sessment and Treatment University of Barcelona Barcelona Spain

Objective: To investigate the association of ischaemic and haemorrhagic strokes with the site of subcortical focal cerebrovascular injuries with affective, behavioural and cognitive dysfunctions in the acute phase and after three months. sample: 58 patients with focal cerebrovascular injuries;mean age 61.5 ± 13.5, 72.4% male. Control group: 20 healthy subjects, mean age 67.1 ± 7.6, 50% male. Results: significant differences were observed (p = 0.006) between the acute phase and three months later on the apathy items of the Neuropsychiatric Inventory (NPI) in patients with subcortical stroke. significant differences were also observed on the affective scale of the BRMs (p = 0.004), the behaviour scale of the Maudsley Obsessive-Compulsive Inventory (MOCI) (p = 0.000), and on the Mini Mental state Examination (MMsE) (p = 0.006). No significant differences were observed on the Hamilton Rating scale-Depression (HRsM) (p = 0.101). significant differences were found according to the infarct type: patients with haemorrhagic lesions had higher raw scores on the HRs-D than those with ischaemic lesions (p = 0.024). Conclusions: The performance of patients with subcortical stroke on affective, behavioural and cognitive scales improves after three months. Patients with haemorrhagic lesions are more likely to be depressive than those with ischaemic lesions.

关键词： subcortical Lesions stroke Cognitive Affective and Behaviour

Foliar Analysis as an Estimate on the Nutritional state of Conilon Coffee Plantations on Cambisoils

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Journal of Life sciences 2014年第2期8卷 181-187页

作者： Alberto Perez Diaz Emesto Castaneda Hidalgo salvador Lozano Trejo Carlos Alberto Bustamante Gonzailez Ramon Antonio Rivera Espinosa Geraldo Rodriguez Ortiz Gloria Martha Martin alonso Cerelino RoblesPerez Guillermo Acosta Coutin Alberto Fernandez Turro Centro de Estudios de Cafe y Cacao Universidad de Guantanamo Guantanamo 95300 Cuba Instituto Tecnologico del Valle de Oaxaca Ex Hacienda de Nazareno Xoxocotlan 712320 Mexico Instituto de Investigaciones Agroforestales UCTB-Tercer Frente Santiago de Cuba 92700 Cuba Instituto Nacional de Ciencias Agricolas San Jose de las Lajas Mayabeque 32700 Cuba Universidad de Ciencias Pedagogicas "Raul Gomez Garcla " Guantanamo 95100 Cuba

The objective of this paper relies on the establishment of the sampling moment and the nutritional state of the species Conilon coffee (Coffea canephora) cultivated in Cambisoils. The effect of different rates of nitrogen fertilization was also studied in the leaves concentrations of N, at randomized complete block designs (N 0 = 0; N 1 = 50; N 2 = 100; N 3 = 150 and N 4 = 200 kg?ha -1 of N) in presence of P (40 kg?ha -1 of P 2 O 5 ) and K (160 kg?ha -1 of K 2 O), with four replicates. The samples were carried out in the months of March (flower blossoming stage), June (fruits growing stage), september (grain development) and December (maturation) in all treatments. Foliar analysis carried out in the month of June (fruits growing stage) for the purpose of establishing critical nutrient range values for N, settling down approaches of interpretation of the same one for the Conilon coffee plantations on Cambisoils. The biggest percentages in the yields are obtained with leaves containing N between 2.80% and 3.10%, a value below 2.80% N which they associated with indicative percentages of stable maximum yield that did not surpass the limits of the adequate nutrients supply.

关键词：咖啡树种植园营养状况叶面果实生长期评估随机区组设计营养状态

在西班牙利用陆地卫星TM影像和地面实测数据估算农作物面积两种方法的比较

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测绘科学 1991年第Z1期22卷 72-76,82页

作者： Federico González alonso salvador López soria José M. Guevas Gozalo 陈常松

本文给出了在那瓦尔(西班牙北部一省)南部地区农作物面积估算的结果。这次估算利用了两种相似但又不同的方法:其一是利用了Ispra EEC遥感应用研究所(IRsA)所创立的区域取样方法,另一种采用美国国家农业统计服务中心(NAss)的区域调查取... 详细信息

本文给出了在那瓦尔(西班牙北部一省)南部地区农作物面积估算的结果。这次估算利用了两种相似但又不同的方法:其一是利用了Ispra EEC遥感应用研究所(IRsA)所创立的区域取样方法,另一种采用美国国家农业统计服务中心(NAss)的区域调查取样方案。两种方法均采用了与陆地卫星TM图像光谱信息相结合的方法。两种方法无论是用直接展开式或回归计算都取得了极为相似的统计估算精度,它们在正方切块估计(IRsA方法)中均获得了较高的相对权重系数。单一作物水平的相关系数值一般较好,并与EEC遥感应用研究所的实验结果相似。

关键词：数据估算 TM影像遥感应用研究农作物面积陆地卫星估算精度光谱信息系数值农业统计南部地区

Preliminary stages before nasal reconstruction using forehead flap:restoring perinasal subunits and nostril patency

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Plastic and Aesthetic Research 2015年第1期2卷 34-37页

作者： Victor Diniz de Pochat Fernando César Câmara de Oliveira Felipe simões da Rocha Mata Marcelo sacramento Cunha Nivaldo alonso JoséValber Lima Meneses Division of Plastic surgery Federal University of BahiaSalvadorBahia 40110Brazil Division of Plastic surgery University of São PauloSão Paulo 14040Brazil

Due to the complex three-dimensional structure of the nose,the repair of the nasal defect requires reconstruction of three different layers:skin envelope,osteocartilaginous framework and nasal lining.Before nasal reconstruction can be accomplished,the nose must rest on a stable platform to avoid late nasal obstructions,and septal deviations resulting from scar contraction.We present three cases of nasal reconstruction using a forehead flap in which we performed a preliminary stage to increase reliability of outcomes.

关键词： Forehead flap nasal reconstruction nostril stenosis preliminary stages

Performance and calibration of quark/gluon-jet taggers using 140 fb^(-1) of pp collisions at √s=13 TeV with the ATLAs detector

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Chinese Physics C 2024年第2期48卷 1-25页

作者： G. Aad B. Abbott K. Abeling N.J. Abicht s.H. Abidi A. Aboulhorma H. Abramowicz H. Abreu Y. Abulaiti B.s. Acharya C. Adam Bourdarios L. Adamczyk s.V. Addepalli M.J. Addison J. Adelman A. Adiguzel T. Adye A.A. Affolder Y. Afik M.N. Agaras J. Agarwala A. Aggarwal C. Agheorghiesei A. Ahmad F. Ahmadov W.s. Ahmed s. Ahuja X. Ai G. Aielli A. Aikot M. Ait Tamlihat B. Aitbenchikh I. Aizenberg M. Akbiyik T.P.A. Åkesson A.V. Akimov D. Akiyama N.N. Akolkar K. Al Khoury G.L. Alberghi J. Albert P. Albicocco G.L. Albouy s. Alderweireldt M. Aleksa I.N. Aleksandrov C. Alexa T. Alexopoulos F. Alfonsi M. Algren M. Alhroob B. Ali H.M.J. Ali s. Ali s.W. Alibocus M. Aliev G. Alimonti W. Alkakhi C. Allaire B.M.M. Allbrooke J.F. Allen C.A. Allendes Flores P.P. Allport A. Aloisio F. alonso C. Alpigiani M. Alvarez Estevez A. Alvarez Fernandez M. Alves Cardoso M.G. Alviggi M. Aly Y. Amaral Coutinho A. Ambler C. Amelung M. Amerl C.G. Ames D. Amidei s.P. Amor Dos santos K.R. Amos V. Ananiev C. Anastopoulos T. Andeen J.K. Anders s.Y. Andrean A. Andreazza s. Angelidakis A. Angerami A.V. Anisenkov A. Annovi C. Antel M.T. Anthony E. Antipov M. Antonelli F. Anulli M. Aoki T. Aoki J.A. Aparisi Pozo M.A. Aparo L. Aperio Bella C. Appelt A. Apyan N. Aranzabal s.J. Arbiol Val C. Arcangeletti A.T.H. Arce E. Arena J-F. Arguin s. Argyropoulos J.-H. Arling O. Arnaez H. Arnold G. Artoni H. Asada K. Asai s. Asai N.A. Asbah J. Assahsah K. Assamagan R. Astalos s. Atashi R.J. Atkin M. Atkinson H. Atmani P.A. Atmasiddha K. Augsten s. Auricchio A.D. Auriol V.A. Austrup G. Avolio K. Axiotis G. Azuelos D. Babal H. Bachacou K. Bachas A. Bachiu F. Backman A. Badea P. Bagnaia M. Bahmani A.J. Bailey V.R. Bailey J.T. Baines L. Baines O.K. Baker E. Bakos D. Bakshi Gupta V. Balakrishnan R. Balasubramanian E.M. Baldin P. Balek E. Ballabene F. Balli L.M. Baltes W.K. Balunas J. Balz E. Banas M. Bandieramonte A. Bandyopadhyay s. Bansal L. Barak M. Barakat E.L. Barberio D. Barberis M. Barbero M.Z. Barel K.N. Barends T. Barillari M-s. Barisits T. Barklow P. Baron D.A. Baron Mo The ATLAs Collaboration

The identification of jets originating from quarks and gluons,often referred to as quark/gluon tagging,plays an important role in various analyses performed at the Large Hadron Collider,as standard Model measurements and searches for new particles decaying to quarks often rely on suppressing a large gluon-induced background.This paper describes the measurement of the efficiencies of quark/gluon taggers developed within the ATLAs Collaboration,using √s=13 TeV proton–proton collision data with an integrated luminosity of 140 fb^(-1) collected by the ATLAs experiment.Two taggers with high performances in rejecting jets from gluon over jets from quarks are studied:one tagger is based on requirements on the number of inner-detector tracks associated with the jet,and the other combines several jet substructure observables using a boosted decision tree.A method is established to determine the quark/gluon fraction in data,by using quark/gluon-enriched subsamples defined by the jet pseudorapidity.Differences in tagging efficiency between data and simulation are provided for jets with transverse momentum between 500 GeV and 2 TeV and for multiple tagger working points.

关键词： ATLAs JET QUARK GLUON TAGGING

Outcomes of critically ill cancer patients with Acinetobacter baumannii infection

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World Journal of Critical Care Medicine 2015年第3期4卷 258-264页

作者： silvio A ?amendys-silva Paulina Correa-García Francisco J García-Guillén María O González-Herrera Américo Pérez-alonso Julia Texcocano-Becerra Angel Herrera-Gómez Patricia Cornejo-Juárez Abelardo Meneses-García Department of Critical Care Medicine Instituto Nacional de Cancerología Department of Critical Care Medicine Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Division of Education and Research Hospital de la Mujer Department of Infectious Diseases Instituto Nacional de Cancerología

AIM: To describe the intensive care unit(ICU) outcomes of critically ill cancer patients with Acinetobacter baumannii(AB) infection.METHODs: This was an observational study that included 23 consecutive cancer patients who acquired AB infections during their stay at ICU of the National Cancer Institute of Mexico(INCan), located in Mexico City. Data collection took place between January 2011, and December 2012. Patients who had AB infections before ICU admission, and infections that occurred during the first 2 d of ICU stay were excluded. Data were obtained by reviewing the electronic health record of each patient. This investigation was approved by the scientific and Ethics Committees at INCan. Because of its observational nature, informed consent of the patients was not required.REsULTs: Throughout the study period, a total of 494 critically ill patients with cancer were admitted to the ICU of the INCan, 23(4.6%) of whom developed AB infections. sixteen(60.9%) of these patients had hematologic malignancies. Most frequent reasons for ICU admission were severe sepsis or septic shock(56.2%) and postoperative care(21.7%). The respiratory tract was the most frequent site of AB infection(91.3%). The most common organ dysfunction observed in our group of patients were the respiratory(100%), cardiovascular(100%), hepatic(73.9%) and renal dysfunction(65.2%). The ICU mortality of patients with 3 or less organ system dysfunctions was 11.7%(2/17) compared with 66.6%(4/6) for the group of patients with 4 or more organ system dysfunctions(P = 0.021). Multivariate analysis identified blood lactate levels(BLL) as the only variable independently associated with inICU death(OR = 2.59, 95%CI: 1.04-6.43, P = 0.040). ICU and hospital mortality rates were 26.1% and 43.5%, respectively.CONCLUsION: The mortality rate in critically ill patients with both HM, and AB infections who are admitted to the ICU is high. The variable most associated with increased mortality was a BLL ≥ 2.6 mmol/L in the first day of stay in the ICU.

关键词： Outcomes Cancer patients Acinetobacter baumannii Intensive care Critical care