Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromosome abnormalities in malignant lymphoma in patients from Kurashiki: histological and immunophenotypic correlations.

Clonal chromosomal abnormalities were found in tumor tissue of 43 (84%) of 51 patients with non-Hodgkin's lymphoma (B-cell, 32; T-cell, 15) from an adult T-cell leukemia/lymphoma-nonendemic area in western mainland Japan. Four tumors were tetraploid, and the other 39 had a chromosome number in the diploid range. Trisomies 3, 5, 7, 18, and X, monosomy 13, and loss of an X in female and a Y in male were found in more than three patients each. Structural abnormalities in arms 1p, 1q, 2q, 3q, 13q, 14q, and 18q were found in eight or more patients each. Clustering of breaks occurred in 3q25-29 (ten patients, nine of whom with a B-cell tumor), 11q13 (five patients), dir dup(12)(q13-15----q21-24) (four patients), 14q32 (12 patients), and 18q21 (seven patients). The 14q32 translocations were all associated with B-cell tumors. t(8;14) was seen in a small noncleaved cell lymphoma, t(11;14)(q13;q32) in one follicular and three intermediately differentiated lymphocytic lymphomas, and t(14;18)(q32;q21) in two follicular lymphomas and one diffuse small cleaved cell tumor. The translocation partner of 14q could not be determined in the other four patients, three of whom had der(18)t(18;? )(q21;? ). The seven 18q21 abnormalities, including a novel translocation t(2;18)(p11;q21.3), all occurred in B-cell tumors; even in the absence of t(14;18), they were closely associated with lymphomas of follicular center cell origin (six of seven).
From Spectrum to Space: The Contribution of Level Difference Cues to Spatial Receptive Fields in the Barn Owl Inferior Colliculus

Space-specific neurons in the owl's inferior colliculus have spatial receptive fields (RFs) computed from interaural time (ITD) and level (ILD) differences. Because of the shape of the owl's head, these cues vary with frequency in a manner specific for each location. We sought to determine the contribution of ILD to spatial selectivity. We measured the normal spatial receptive fields of space-specific neurons using virtual sound sources (i.e., noises filtered to simulate external sound sources, presented using headphones). The virtual-source filters were then altered so that ITD was fixed while frequency-specific ILDs varied according to location in the usual manner. The resulting “ILD-alone” RF typically revealed a horizontal band of excitation that included the normal RF. Above and below, the neurons were inhibited. Interestingly, the maxima of ILD-alone RFs were generally outside the normal RF, suggesting that space-specific neurons are not optimally tuned to the ILD spectrum occurring at the normal RF location. Congruously, frequency-specific ILD tuning, assessed with tones, better matched the ILDs at the peak of the ILD-alone RF than those at the peak of the normal RF. The firing evoked from the normal RF may thus reflect the balance of excitatory and inhibitory inputs needed to appropriately restrict the receptive field. Frequency-specific ILD tuning curves were combined with measured head-filtering characteristics to predict responses to the frequency-specific ILDs at each location. The predicted ILD-alone RFs, which are based on a simple sum of frequency-specific inputs, accounted for 56% of the variance in our measured ILD-alone RFs.
Weather Variability in the Vicinity of Waste Dump-Sites in Benin City

This study examines the contribution of dump-sites to weather variability in Benin City. By utilizing the experimental research design, the researcher collected primary data for waste volumes, GHGs, and temperature across the study sites for a period of three months. Analysis of variance (ANOVA) and multiple linear regressions (MLR) were employed for data analysis. Findings revealed that highly populated areas such as, Iguomo (7.7%), Ekehuan (7.8%), GRA (6.8%) and New-Benin (9.2%) generated the greater proportion of waste in the area. The ANOVA analysis showed that temperature is significantly different as distance increase from dump site at P<0.05 indicating the influence of waste dumps on temperature in the area. Nevertheless, the MLR identified that temperature attained at the various dump sites significantly depended on the GHGs emitted at the sites at P<0.05. The study as a result of findings, advocates waste re-use & recycle; and establishment of waste treatment plants amongst others in the area.
Ulcerative Colitis and Perfluorooctanoic Acid (PFOA) in a Highly Exposed Population of Community Residents and Workers in the Mid-Ohio Valley

Background: Little is known about environmental determinants of autoimmune diseases. Objectives: We studied autoimmune diseases in relation to level of exposure to perfluorooctanoic acid (PFOA), which was introduced in the late 1940s and is now ubiquitous in the serum of residents of industrialized countries. Methods: In 2008–2011 we interviewed 32,254 U.S. adults with high serum PFOA serum levels (median, 28 ng/mL) associated with drinking contaminated water near a chemical plant. Disease history was assessed retrospectively from 1952 or birth (if later than 1952) until interview. Self-reported history of autoimmune disease was validated via medical records. Cumulative exposure to PFOA was derived from estimates of annual mean serum PFOA levels during follow-up, which were based on plant emissions, residential and work history, and a fate-transport model. Cox regression models were used to estimate associations between quartiles of cumulative PFOA serum levels and the incidence of autoimmune diseases with ≥ 50 validated cases, including ulcerative colitis (n = 151), Crohn’s disease (n = 96), rheumatoid arthritis (n = 346), insulin-dependent diabetes (presumed to be type 1) (n = 160), lupus (n = 75), and multiple sclerosis (n = 98). Results: The incidence of ulcerative colitis was significantly increased in association with PFOA exposure, with adjusted rate ratios by quartile of exposure of 1.00 (referent), 1.76 (95% CI: 1.04, 2.99), 2.63 (95% CI: 1.56, 4.43), and 2.86 (95% CI: 1.65, 4.96) (ptrend < 0.0001). A prospective analysis of ulcerative colitis diagnosed after the baseline 2005–2006 survey (n = 29 cases) suggested a positive but non-monotonic trend (ptrend = 0.21). Discussion: To our knowledge, this is the first study of associations between this common environmental exposure and autoimmune diseases in humans. We found evidence that PFOA is associated with ulcerative colitis.
CGD Working Paper # 120 April 2007 Performance-Based Incentives for Health : Conditional Cash Transfer Programs in Latin America and the Caribbean

In order to support poor families in the developing world to seek and use health care, a multi-pronged strategy is needed on both the supply and the demand side of health care. A demand-side program called Conditional Cash Transfers (CCTs) strives to reduce poverty and also increase food consumption, school attendance, and use of preventive health care. Since 1997, seven countries in Latin America have implemented and evaluated CCT programs with health and nutrition components. The core of the program is based on encouraging poor mothers to seek preventive health services and attend health education talks by providing a cash incentive for their healthy behavior (with healthy behavior representing performance). Evaluations of these programs measured outputs in the utilization of services; health knowledge, attitudes, and practice; food consumption; the supply and quality of services; as well as outcomes in vaccination rates; nutritional status; morbidity; mortality; and fertility. While CCT impact evaluations provided unambiguous evidence that financial incentives increase utilization of key services by the poor, the studies gave little attention to the impact on health-related behaviors, attitudes, and household decision-making or how these factors contribute to or limit impact on health outcomes. Recommendations include expanding the scope of future evaluations to study these effects, modeling program effects beforehand, and carefully selecting the conditions for payment so that they are not too burdensome yet not irrelevant. Continuing to focus on the extreme poor is recommended since findings show that the poorest households must reach a minimum level of food consumption before they are able to make other investments in their health and well-being. The Center for Global Development is an independent think tank that works to reduce global poverty and inequality through rigorous research and active engagement with the policy community. Use and dissemination of this Working Paper is encouraged, however reproduced copies may not be used for commercial purposes. Further usage is permitted under the terms of the Creative Commons License. This paper was made possible in part by funding from the Bill & Melinda Gates Foundation. The views expressed in this paper are those of the author and should not be attributed to the directors or funders of the Center for Global Development.
Taxonomic status of the enigmatic salamander Cryptotriton adelos (Amphibia: Plethodontidae) from northern Oaxaca, Mexico, with observations on its skull and postcranial skeleton

DAVID B. WAKE, SEAN M. ROVITO, JESSICA A. MAISANO & JAMES HANKEN 4 Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720-3160, USA. E-mail:wakelab@berkeley.edu; smrovito@gmail.com Jackson School of Geosciences, University of Texas, Austin, Texas 78712, USA. E-mail: maisano@mail.utexas. edu Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA. E-mail: hanken@oeb.harvard. edu Corresponding author. E-mail: hanken@oeb.harvard. edu
Unbiased offline evaluation of contextual-bandit-based news article recommendation algorithms

Contextual bandit algorithms have become popular for online recommendation systems such as Digg, Yahoo! Buzz, and news recommendation in general. Offline evaluation of the effectiveness of new algorithms in these applications is critical for protecting online user experiences but very challenging due to their "partial-label" nature. Common practice is to create a simulator which simulates the online environment for the problem at hand and then run an algorithm against this simulator. However, creating simulator itself is often difficult and modeling bias is usually unavoidably introduced. In this paper, we introduce a replay methodology for contextual bandit algorithm evaluation. Different from simulator-based approaches, our method is completely data-driven and very easy to adapt to different applications. More importantly, our method can provide provably unbiased evaluations. Our empirical results on a large-scale news article recommendation dataset collected from Yahoo! Front Page conform well with our theoretical results. Furthermore, comparisons between our offline replay and online bucket evaluation of several contextual bandit algorithms show accuracy and effectiveness of our offline evaluation method.
Some evolutionary patterns of palaeokarst developed in Pleistocene deposits (Ebro Basin, NE Spain): Improving geohazard awareness in present‐day karst

Pleistocene detrital deposits in the central Ebro Basin frequently show deformation features due mainly to karstification in the underlying Neogene evaporites. In 123 cases, estimation of parameters of shape and minimum volume of materials involved was accomplished. Six of them were analysed in more detail to establish the main processes involved in their genesis and the succession of events. All the deformation features in the selected sites are synsedimentary. To achieve the objectives, intense fieldwork was made applying methods of sedimentology and structural geology. Usually, a complex evolutionary pattern was observed, with evidences of dissolution, sagging, collapse, gravity flow, suffosion, and plastic flow. In a schematic way, three main situations, independent of the age of the analysed deposits, can be distinguished: (a) slow subsidence, (b) collapse, and (c) temporal overlapping of both processes. In the first 2 scenarios, basins with smooth or abrupt borders, respectively, were generated on the land surface. In the third one, slow subsidence was followed by a collapse, located in the area of maximum flexure. These patterns are also observed in present‐day dolines. Comparison of direct and indirect parameters between paleodolines and present‐day dolines indicates a bigger size of the latter, probably caused by the different conditions of observation. This study helps to know the possibilities in the evolution of mantled karst features, to estimate the volume of material affected by karstification and to improve the knowledge of present‐day dolines behaviour. Consequently, study of paleodolines must be considered to achieve a better urban planning in active karstic areas.
Protein Supplementation and the Incidence of Apoptosis and Oxidative Stress in Mouse Embryos

OBJECTIVE: To estimate the effect of protein supplementation of culture media on reactive oxygen species production and incidence of apoptosis in preimplantation mouse embryos. METHODS: A total of 72 two-cell mouse embryos were cultured in human tubal fluid (HTF) alone (HTF-alone, control) and 71 embryos in HTF with protein supplementation (10% serum substitute supplement; HTF-SSS) for 72 hours. Total cell number per embryo was determined by staining with Hoechst 33258. Allocation of inner cell mass and trophectoderm in blastocysts and incidence of apoptosis were determined by confocal microscopy. Levels of reactive oxygen species in culture media were measured by chemiluminescence assay using luminol as probe. RESULTS: Blastocyst development, total cell number, and the inner cell mass/trophectoderm ratio were similar between the 2 groups. The blastocyst hatching rate was significantly higher in the HTF-SSS group than in the HTF-alone group (20% compared with 4%, P = .007). Level of reactive oxygen species was significantly higher in HTF-alone compared with HTF-SSS at 24 hours (median and interquartile range 28 [13, 43] compared with 0 [0, 1], P = .02), 48 hours (24 [21, 26] compared with 2 [1, 2], P = .02), and 72 hours (26 [9, 32] compared with 2 [2, 3], P = .03). The incidence of apoptosis in blastocysts cultured in HTF-SSS was significantly lower than those in HTF-alone group (mean ± standard deviation 2.38 ± 0.68 and 5.81 ± 1.11, respectively, P = .001). CONCLUSION: Protein supplementation of culture media improves the hatching rate and reduces reactive oxygen species levels and the incidence of apoptosis in mouse preimplantation embryos.
Huntingtin-Interacting Protein 1 Influences Worm and Mouse Presynaptic Function and Protects Caenorhabditis elegans Neurons against Mutant Polyglutamine Toxicity

Huntingtin-interacting protein 1 (HIP1) was identified through its interaction with htt (huntingtin), the Huntington's disease (HD) protein. HIP1 is an endocytic protein that influences transport and function of AMPA and NMDA receptors in the brain. However, little is known about its contribution to neuronal dysfunction in HD. We report that the Caenorhabditis elegans HIP1 homolog hipr-1 modulates presynaptic activity and the abundance of synaptobrevin, a protein involved in synaptic vesicle fusion. Presynaptic function was also altered in hippocampal brain slices of HIP1−/− mice demonstrating delayed recovery from synaptic depression and a reduction in paired-pulse facilitation, a form of presynaptic plasticity. Interestingly, neuronal dysfunction in transgenic nematodes expressing mutant N-terminal huntingtin was specifically enhanced by hipr-1 loss of function. A similar effect was observed with several other mutant proteins that are expressed at the synapse and involved in endocytosis, such as unc-11/AP180, unc-26/synaptojanin, and unc-57/endophilin. Thus, HIP1 is involved in presynaptic nerve terminal activity and modulation of mutant polyglutamine-induced neuronal dysfunction. Moreover, synaptic proteins involved in endocytosis may protect neurons against amino acid homopolymer expansion.
Prophylactic Infusions of Phenylephrine and Ephedrine during Combined Spinal Epidural Anaesthesia for Caesarean Section: A Comparative Study

Background: Hypotension is the most common adverse effect in parturients after spinal anaesthesia for Caesarean section. Despite various pharmacological and non-pharmacological methods used in its prevention and treatment, vasopressors have become very important in the management of this form of hypotension. Objective: This study was aimed at comparing the efficacy and safety of prophylactic intravenous infusions of phenylephrine and ephedrine at preventing maternal hypotension during Combined Spinal Epidural anaesthesia (CSE) for Caesarean section. Methods: Sixty ASA I and II patients scheduled for elective Caesarean section, were randomly allocated into two groups. Patients in Group I received Phenylephrine 80 μg/min while patients in Group II received Ephedrine 1 mg/min immediately after the subarachnoid 10 mg plain bupivacaine injection while the epidural catheter was being inserted and secured. All the patients received a crystalloid preload of 1 litre of 0.9% normal saline prior to the induction of CSE. Results: The overall incidence of hypotension was 8.5% (6.7% in the phenylephrine group and 10.3% in the ephedrine groups). The lowest systolic (105.8 ± 9.2 mmHg) and diastolic arterial pressures (60.9 ± 8.9 mmHg) occurred in the ephedrine group while the lowest heart rates occurred in the phenylephrine group. The mean umbilical artery pH was 7.3 while Apgar scores at 1st and 5th min were essentially the same in the two groups. Conclusion: Prophylactic intravenous infusions of phenylephrine and ephedrine are safe and effective at reducing the incidence and severity of hypotension during combined spinal epidural anaesthesia for elective Caesarean section with no associated neonatal acidosis.
Cloning and mRNA expression of vascular endothelial growth factor in ischemic retinas of Macaca fascicularis.

PURPOSE To identify and isolate cDNAs for the alternatively spliced vascular endothelial growth factor (VEGF) mRNAs present in retina and to compare the relative levels of the splice variants and localization of VEGF mRNA in nonischemic and ischemic adult simian retinas. METHODS Retinas of cynomolgous monkeys were made ischemic by laser occlusion of the main branch retinal veins. Reverse transcription-polymerase chain reaction was used to amplify the VEGF coding region of RNA from ischemic and control retinas, and amplification products were analyzed by agarose gel electrophoresis, Southern blot, and nucleotide sequencing. Analysis of VEGF mRNA expression was accomplished by in situ hybridization. RESULTS Control and ischemic retinas produce mRNAs that correspond to the 121 and 165 amino acid diffusible isoforms of VEGF, and relatively low levels of VEGF189, the heparin-binding isoform. There was no significant difference in the levels of the alternatively spliced VEGF transcripts between control and ischemic retinas. Cloning and sequencing revealed that simVEGF cDNAs are 99% identical to human VEGFs and are predicted to encode proteins identical to their respective human homologues. In situ hybridization of nonischemic retinas revealed a low level of VEGF mRNA in retinal ganglion cells and in the inner nuclear layer. VEGF mRNA levels were elevated in ischemic retinas as early as 1 day after laser vein occlusion, when there was a small but reproducible increase in signal. The expression peaked at approximately 13 days, coincident with maximal iris neovascularization, and was significantly reduced by 28 days, when the iris vessels largely regressed. CONCLUSIONS The elevation of simVEGF121 and VEGF165 in ischemic retinas is consistent with a role for diffusible, retina-derived angiogenic factors in the development of ocular neovascularization.
Good enough practices in scientific computing

Author summary Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start. This paper presents a set of good computing practices that every researcher can adopt, regardless of their current level of computational skill. These practices, which encompass data management, programming, collaborating with colleagues, organizing projects, tracking work, and writing manuscripts, are drawn from a wide variety of published sources from our daily lives and from our work with volunteer organizations that have delivered workshops to over 11,000 people since 2010.
Varenicline and suicidal behaviour: a cohort study based on data from the General Practice Research Database

Objective To determine whether varenicline, a recently licensed smoking cessation product, is associated with an increased risk of suicide and suicidal behaviour compared with alternative treatments bupropion and nicotine replacement therapy. Design Cohort study nested within the General Practice Research Database. Setting Primary care in the United Kingdom. Participants 80 660 men and women aged 18-95 years were prescribed a new course of a smoking cessation product between 1 September 2006 and 31 May 2008; the initial drugs prescribed during follow-up were nicotine replacement products (n=63 265), varenicline (n=10 973), and bupropion (n=6422). Main outcome measures Primary outcomes were fatal and non-fatal self harm, secondary outcomes were suicidal thoughts and depression, all investigated with Cox’s proportional hazards models. Results There was no clear evidence that varenicline was associated with an increased risk of fatal (n=2) or non-fatal (n=166) self harm, although a twofold increased risk cannot be ruled out on the basis of the upper limit of the 95% confidence interval. Compared with nicotine replacement products, the hazard ratio for self harm among people prescribed varenicline was 1.12 (95% CI 0.67 to 1.88), and it was 1.17 (0.59 to 2.32) for people prescribed bupropion. There was no evidence that varenicline was associated with an increased risk of depression (n=2244) (hazard ratio 0.88 (0.77 to1.00)) or suicidal thoughts (n=37) (1.43 (0.53 to 3.85)). Conclusion Although a twofold increased risk of self harm with varenicline cannot be ruled out, these findings provide some reassurance concerning its association with suicidal behaviour.
A holistic in silico approach to predict functional sites in protein structures

MOTIVATION Proteins execute and coordinate cellular functions by interacting with other biomolecules. Among these interactions, protein-protein (including peptide-mediated), protein-DNA and protein-RNA interactions cover a wide range of critical processes and cellular functions. The functional characterization of proteins requires the description and mapping of functional biomolecular interactions and the identification and characterization of functional sites is an important step towards this end. RESULTS We have developed a novel computational method, Multi-VORFFIP (MV), a tool to predicts protein-, peptide-, DNA- and RNA-binding sites in proteins. MV utilizes a wide range of structural, evolutionary, experimental and energy-based information that is integrated into a common probabilistic framework by means of a Random Forest ensemble classifier. While remaining competitive when compared with current methods, MV is a centralized resource for the prediction of functional sites and is interfaced by a powerful web application tailored to facilitate the use of the method and analysis of predictions to non-expert end-users. AVAILABILITY http://www.bioinsilico. org/MVORFFIP