Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of low levels of lice and internal nematodes on weight gain and blood parameters in calves in central Texas.

The effects of low levels of both biting and sucking lice, a mixed population of nematodes, and a combination of all these parasites were evaluated in calves held in a barn with no environmental controls in central Texas. Observations at 122 sites on each animal for 16 wk consecutively in 1987 revealed that the largest numbers of all louse species [Haematopinus eurysternus (Nitzsch). Linognathus vituli (L.), and Bovicola bovis (L.)] occurred 3-7 wk after infestation. In 1988 L. vituli populations decreased rapidly after the 3rd wk and B. bovis remained fairly constant for 20 wk consecutively. Average nematode egg counts increased to approximately 300 eggs per gram of feces in 1987 and approximately 600 eggs per gram of feces in 1988. The nematodes Ostertagia ostertagia, Haemonchus placei, Oesophagostomum radiatum, Cooperia spp. , and Trichostrongylus spp. were present at the end of the study in both years as determined by necropsy. No significant differences in erythrocyte count, mean cell volume, hematocrit, hemoglobin concentration, leukocyte counts, or serum albumin concentration were detected. However, significant increases in total serum protein concentration and serum globulin levels in calves harboring both groups of parasites were observed. Mean weight gain in calves infested with lice and nematodes was 11.4 and 10 kg less than that of uninfested controls during 16 wk in 1987 and 20 wk in 1988, respectively.
Dispersal Patterns, Dispersal Mechanisms, and Invasion Wave Speeds for Invasive Thistles

Understanding and predicting population spread rates is an important problem in basic and applied ecology. In this article, we link estimates of invasion wave speeds to species traits and environmental conditions. We present detailed field studies of wind dispersal and compare nonparametric (i.e., data‐based) and mechanistic (fluid dynamics model–based) dispersal kernel and spread rate estimates for two important invasive weeds, Carduus nutans and Carduus acanthoides. A high‐effort trapping design revealed highly leptokurtic dispersal distributions, with seeds caught up to 96 m from the source, far further than mean dispersal distances (approx. 2 m). Nonparametric wave speed estimates are highly sensitive to sampling effort. Mechanistic estimates are insensitive to sampling because they are obtained from independent data and more useful because they are based on the dispersal mechanism. Over a wide range of realistic conditions, mechanistic spread rate estimates were most sensitive to high winds and low seed settling velocities. The combination of integrodifference equations and mechanistic dispersal models is a powerful tool for estimating invasion spread rates and for linking these estimates to characteristics of the species and the environment.
Comparative analyses of human immunodeficiency virus type 1 (HIV-1) and HIV-2 Vif mutants

Virion infectivity factor (vif), a gene found in all lentiviruses, plays an essential role in virus replication in certain target cells. We examined the replication competence of the human immunodeficiency virus type 2 (HIV-2) vif mutant in different T-cell lines and primary cells in comparison with that of the HIV-1 vif mutant. Both mutant viruses were unable to replicate in peripheral blood-derived mononuclear cells but replicated with wild-type efficiency in certain T-cell lines, such as SupT1 and MOLT-4/8. These results confirm the importance of vif in the infection of relevant target cells and imply that some cellular factor(s) could compensate for vif function. However, HIV-1 and HIV-2 vif mutant viruses also show differential replications in other cell lines, suggesting either different threshold requirements for the same cellular factor(s) or the involvement of different factors to compensate for vif-1 and vif-2 functions. By cross complementation experiments, we showed that vif-1 and vif-2 have similar functions. Our studies further indicate the existence of two kinds of nonpermissive cells: H9 is unable to complement HIV-1 delta vif but is susceptible to a one-round infection with HIV-1 delta vif produced from permissive cells. In contrast, U937 is nonpermissive for HIV-2 delta vif produced from permissive cells but, once infected, is able to complement the delta vif function. In both types of nonpermissive cells, a step prior to proviral DNA synthesis is affected.
Prognostic Factors of Prostate Cancer in Tunisian Men: Immunohistochemical Study.

BACKGROUND Prostate cancer is the second most common male cancer and remains a leading cause of cancer death worldwide. Heterogeneity regarding recurrence, tumor progression and therapeutic response reflects the inadequacy of traditional prognostic factors and underlies interest in new genetic and molecular markers. In this work, we studied the prognostic value of the expression of 9 proteins, Ki-67, p53, Bcl-2, PSA, HER2, E-cadherin, p21WAF1/Cip1, p27Kip1 and p16ink4a in prostate cancer. MATERIALS AND METHODS We conducted a retrospective study of 50 prostate cancers diagnosed in Pathology Department of Farhet Hached Hospital, Sousse, Tunisia, during a period of 12 months. Clinico-pathological data and survival were investigated. Protein expression was analyzed by immunohistochemistry on archived material. RESULTS Expression or over-expression of Ki-67, p53, Bcl-2, PSA, HER2, E-Cadherin, p21WAF1/Cip1, p27Kip1 and p16ink4a was observed in 68%, 24%, 32%, 78%, 12%, 90%, 20%, 44% and 56% of cases, respectively. Overall five-year survival was 68%. A statistically significant correlation was observed between death occurrence and advanced age (p=0.018), degree of tumor differentiation (p=0.0001), perineural invasion (p=0.016) and metastasis occurrence (p=0.05). Death occurrence was significantly correlated with the expression of p53 (p=0.007), Bcl-2 (p=0.02), Ki-67 (p=0.05) and p27Kip1 (p=0.04). CONCLUSIONS The p53, Bcl-2, Ki-67 and p27Kip1 proteins may be useful additional prognostic markers for prostate cancer. The use of these proteins in clinical practice can improve prognosis prediction, disease screening and treatment response of prostatic cancer.
The Influence of Different Criteria for Establishing Optimal Cutoff Scores on Performance of Two Self-Report Measures for Warzone PTSD

Posttraumatic stress disorder (PTSD) has been regarded as a signature injury of war and elevated to one of the major behavioral health problems faced by military service members and veterans deployed to warzones. In PTSD diagnosis, self-report measures have often been used with a cutoff score to identify those with an elevated likelihood of having PTSD prior to conducting a second-tier diagnostic interview. With an attempt to guide the selection of cutoffs in self-report PTSD measures for various purposes, this study examined how five common criteria for establishing an optimal cutoff influenced the performance of self-report measures for warzone PTSD in relation to the Clinician Administered PTSD Scale for Diagnostic and Statistical Manual of Mental Disorders, 5th edition (DSM–5) and whether the influence differed for the PTSD Checklist for DSM–5 and the Mississippi Scale for Combat-Related PTSD. Using a probability sample of Vietnam theater veterans in the National Vietnam Veterans Longitudinal Study, results showed that in both self-report measures, the Youden Index criterion yielded the optimal cutoff that led to better test performance.
Using Diurnal Temperature Signals to Infer Vertical Groundwater‐Surface Water Exchange

Heat is a powerful tracer to quantify fluid exchange between surface water and groundwater. Temperature time series can be used to estimate pore water fluid flux, and techniques can be employed to extend these estimates to produce detailed plan‐view flux maps. Key advantages of heat tracing include cost‐effective sensors and ease of data collection and interpretation, without the need for expensive and time‐consuming laboratory analyses or induced tracers. While the collection of temperature data in saturated sediments is relatively straightforward, several factors influence the reliability of flux estimates that are based on time series analysis (diurnal signals) of recorded temperatures. Sensor resolution and deployment are particularly important in obtaining robust flux estimates in upwelling conditions. Also, processing temperature time series data involves a sequence of complex steps, including filtering temperature signals, selection of appropriate thermal parameters, and selection of the optimal analytical solution for modeling. This review provides a synthesis of heat tracing using diurnal temperature oscillations, including details on optimal sensor selection and deployment, data processing, model parameterization, and an overview of computing tools available. Recent advances in diurnal temperature methods also provide the opportunity to determine local saturated thermal diffusivity, which can improve the accuracy of fluid flux modeling and sensor spacing, which is related to streambed scour and deposition. These parameters can also be used to determine the reliability of flux estimates from the use of heat as a tracer.
Variation in Human Islet Viability Based on Different Membrane Integrity Stains

Membrane integrity fluorescent staining is used routinely to evaluate islet viability. Results are used as one of the determining factors in islet product release criteria, and are used to assess the efficacy of different culture conditions. Recently, it has been observed that there is variation in the viability staining of freshly isolated islets based on which viability assay is used. This investigation compares three membrane integrity stains for the viability assessment of isolated human islets. Fluorescein diacetate/propidium iodide (FDA/PI), the current standard method for assessing islet viability, demonstrates intense extracellular fluorescence, reducing the differential staining of intact islets. We further evaluated SYTO-13/ethidium bromide (SYTO/EB) and calcein AM/ethidium homodimer (C/EthD) as alternative viability assays, and found considerable variation between FDA/PI and either SYTO/EB or C/EthD staining. Preparations of human islets were obtained from cadaveric pancreata after collagenase digestion, mechanical separation, and purification by continuous Ficoll gradient centrifugation. For each preparation, two replicate samples of 50 islets were counted for each stain, and the percent viability calculated. The results for SYTO/EB and C/EthD were nearly identical [57.6 ± 7.3% and 57.9 ± 7.2%, respectively (mean ± SEM), N = 11]. FDA/PI-stained islets, however, showed consistently elevated values when compared to SYTO/EB. Accurate assessment of islet viability remains a critical determinant of islet product release. The discrepancies found between FDA/PI scoring and visual quality, compared with alternative stains, suggests that the FDA/PI stain may not be the optimal approach to assess islet viability.
Testing for genetic association in the presence of population stratification in genome‐wide association studies

Genome‐wide case‐control association study is gaining popularity, thanks to the rapid development of modern genotyping technology. In such studies, population stratification is a potential concern especially when the number of study subjects is large as it can lead to seriously inflated false‐positive rates. Current methods addressing this issue are still not completely immune to excess false positives. A simple method that corrects for population stratification is proposed. This method modifies a test statistic such as the Armitage trend test by using an additive constant that measures the variation of the effect size confounded by population stratification across genomic control (GC) markers. As a result, the original statistic is deflated by a multiplying factor that is specific to the marker being tested for association. This deflating multiplying factor is guaranteed to be larger than 1. These properties are in contrast to the conventional GC method where the original statistic is deflated by a common factor regardless of the marker being tested and the deflation factor may turn out to be less than 1. The new method is introduced first for regular case‐control design and then for other situations such as quantitative traits and the presence of covariates. Extensive simulation study indicates that this new method provides an appealing alternative for genetic association analysis in the presence of population stratification. Genet. Epidemiol. 33:637–645, 2009. © 2009 Wiley‐Liss, Inc.
Prognostic Association of Circulating Neutrophil Count with No-Reflow in Patients with ST-Segment Elevation Myocardial Infarction following Successful Primary Percutaneous Intervention

Objective The aim of the present study was to investigate the predictive value of neutrophil count for no-reflow in patients with ST-segment elevation myocardial infarction (STEMI) who underwent successful primary percutaneous intervention (PCI). Methods We conducted a retrospective study of 361 patients diagnosed with acute STEMI between 2011 and 2015. All patients underwent successful PCI within 12 h from the onset of symptoms. Angiographic no-reflow was diagnosed based on a post-PCI thrombolysis in myocardial infarction flow grade ≤ 2 without mechanical obstruction. According to a neutrophil count cut-off determined by receiver operating characteristic curve analysis, patients were divided into two groups: group A (neutrophil count < 9.14 × 109/L) and group B (neutrophil count ≥ 9.14 × 109/L). Results Compared to patients in the normal reflow group, patients with no-reflow had higher neutrophil counts (P < 0.05). The incidence rate of no-reflow in group A (18, 9.3%) was significantly lower than that in group B (38). Multivariate logistic regression analysis revealed that a neutrophil count ≥ 9.14 × 109/L was independently predictive for no-reflow (odds ratio = 4.474, 95% confidence interval: 1.610–12.433, P = 0.004) after adjusting for potential confounders. Conclusions A circulating neutrophil count ≥ 9.14 × 109/L is independently associated with no-reflow in patients with acute STEMI following primary PCI.
Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

Abstract The discovery of microRNAs (miRNAs) remains an important problem, particularly given the growth of high-throughput sequencing, cell sorting and single cell biology. While a large number of miRNAs have already been annotated, there may well be large numbers of miRNAs that are expressed in very particular cell types and remain elusive. Sequencing allows us to quickly and accurately identify the expression of known miRNAs from small RNA-Seq data. The biogenesis of miRNAs leads to very specific characteristics observed in their sequences. In brief, miRNAs usually have a well-defined 5′ end and a more flexible 3′ end with the possibility of 3′ tailing events, such as uridylation. Previous approaches to the prediction of novel miRNAs usually involve the analysis of structural features of miRNA precursor hairpin sequences obtained from genome sequence. We surmised that it may be possible to identify miRNAs by using these biogenesis features observed directly from sequenced reads, solely or in addition to structural analysis from genome data. To this end, we have developed mirnovo, a machine learning based algorithm, which is able to identify known and novel miRNAs in animals and plants directly from small RNA-Seq data, with or without a reference genome. This method performs comparably to existing tools, however is simpler to use with reduced run time. Its performance and accuracy has been tested on multiple datasets, including species with poorly assembled genomes, RNaseIII (Drosha and/or Dicer) deficient samples and single cells (at both embryonic and adult stage).
Hurricane Katrina Deaths, Louisiana, 2005

ABSTRACT Objective: Hurricane Katrina struck the US Gulf Coast on August 29, 2005, causing unprecedented damage to numerous communities in Louisiana and Mississippi. Our objectives were to verify, document, and characterize Katrina-related mortality in Louisiana and help identify strategies to reduce mortality in future disasters. Methods: We assessed Hurricane Katrina mortality data sources received in 2007, including Louisiana and out-of-state death certificates for deaths occurring from August 27 to October 31, 2005, and the Disaster Mortuary Operational Response Team's confirmed victims' database. We calculated age-, race-, and sex-specific mortality rates for Orleans, St Bernard, and Jefferson Parishes, where 95% of Katrina victims resided and conducted stratified analyses by parish of residence to compare differences between observed proportions of victim demographic characteristics and expected values based on 2000 US Census data, using Pearson chi square and Fisher exact tests. Results: We identified 971 Katrina-related deaths in Louisiana and 15 deaths among Katrina evacuees in other states. Drowning (40%), injury and trauma (25%), and heart conditions (11%) were the major causes of death among Louisiana victims. Forty-nine percent of victims were people 75 years old and older. Fifty-three percent of victims were men; 51% were black; and 42% were white. In Orleans Parish, the mortality rate among blacks was 1.7 to 4 times higher than that among whites for all people 18 years old and older. People 75 years old and older were significantly more likely to be storm victims (P < .0001). Conclusions: Hurricane Katrina was the deadliest hurricane to strike the US Gulf Coast since 1928. Drowning was the major cause of death and people 75 years old and older were the most affected population cohort. Future disaster preparedness efforts must focus on evacuating and caring for vulnerable populations, including those in hospitals, long-term care facilities, and personal residences. Improving mortality reporting timeliness will enable response teams to provide appropriate interventions to these populations and to prepare and implement preventive measures before the next disaster. (Disaster Med Public Health Preparedness. 2008;2:215–223)
Conductive interstitial thermal therapy device for surgical margin ablation: In vivo verification of a theoretical model

Purpose: To demonstrate the efficacy and predictability of a new conductive interstitial thermal therapy (CITT) device to ablate surgical margins. Method: The temperature distributions during thermal ablation of CITT were calculated with finite element modelling in a geometrical representation of perfused tissue. The depth of ablation was derived using the Arrhenius and the Sapareto and Dewey (S&D) models for the temperature range of 90 to 150°C. The female pig animal model was used to test the validity of the mathematical model. Breast tissues were ablated to temperatures in the range of 79–170°C, in vivo. Triphenyltetrazolium chloride viability stain was used to delineate viable tissue from ablated regions and the ablation depths were measured using digital imaging. Results: The calculations suggest that the CITT can be used to ablate perfused tissues to a 10–15 mm width within 20 minutes. The measured and calculated depths of ablation were statistically equivalent (99% confidence intervals) within ± 1mm at 170°C. At lower temperatures the equivalence between the model and the observations was within ± 2 mm. Conclusion: The CITT device can reliably and uniformly ablate a 10–15 mm wide region of soft tissue. Thus, it can be used to secure negative margins following the resection of a primary tumor, which could impede local recurrences in the treatment of local diseases such as early staged, non-metastatic, breast cancer.
Efficacy and safety of the haemostasis achieved by Vivostat system during laparoscopic partial nephrectomy.

INTRODUCTION Haemostasis remains the greatest challenge during laparoscopic partial nephrectomy. We describe the use of the Vivostat system helping effective haemostasis during laparoscopic partial nephrectomy (LPN). PATIENTS AND METHOD Twenty-eight patients underwent LPN. Autologous fibrin sealant was prepared with the Vivostat system and applied to the resection bed. This system is an automated medical device for the preparation of an autologous fibrin sealant from the patient's blood. Pre and postoperative clinical parameters and laboratory values were evaluated, for acute and delayed bleeding. RESULTS Median patient's age was 58 years (range, 25-75). All patients underwent LPN for renal tumors (mean size 2.5 cm; range 0.9-4.5 cm). Six resection were performed without vessels clamping, and 22 were realized with selective arterial Bulldog clamping. Haemostasis was achieved by a cellulose bolster (80%), by stitches (67%) and by sealant application after declamping (100%) (mean amount applied: 5.1 ml). The mean warm ischemia time was 26 minutes (range, 16-45) for 22 interventions. Mean blood loss was 128 cc (range, 20-500). Pre-operative and post-operative creatinine values (mean, 0.91 vs. 1 ng/mi) did not differ significantly; whereas mean Hb levels slightly decreases after surgery (mean, 14.7 vs. 12.5 g/dl). Mean operative time was 131 minutes (range, 60-190). All but one had negative surgical margins. One intraoperative bleeding occurred needing blood transfusion (1 unit). Postoperatively, we observed only 1 perirenal hematoma treated conservatively requiring blood transfusion. CONCLUSIONS In this study, an effective haemostasis was achieved and maintained after kidney reperfusion. These data support the previous finding with the same system and encourage its use in LPN.
Pectin-fermenting Bacteria Isolated from the Bovine Rumen

Thirty-two strains of pectin-fermenting rumen bacteria were isolated from bovine rumen contents in a rumen fluid medium which contained pectin as the only added energy source. Based on differences in morphology and the Gram stain, 10 of these strains were selected for characterization. Two strains were identified as Lachnospira multiparus, four strains were identified as Butyrivbrio fibrisolvens, and three strains were identified as Bacteroides ruminicola. Characteristics of the remaining strain did not correspond with any previously described species. It was a gram-positive anaerobic coccus, 1.0 to 1.2 μm in diameter, and occurred primarily as single cells or diplococci. The strain fermented pectin rapidly but showed little or no growth on any other energy sources tested. The only detectable end products were acetic acid and gas, a portion of which was identified as hydrogen. Although the physiological characteristics of this organism differ markedly from other described species, it has been placed in the genus Peptostreptococcus on the basis of morphology, Gram stain, relations to oxygen, and the occurrence of cell division in only one plane. End products of fermentation are somewhat similar to those of the cellulolytic ruminococci. Eight previously characterized strains of cellulolytic bacteria isolated in nonselective media were unable to ferment pectin, whereas ten strains of hemicellulolytic rumen bacteria, eight of which were isolated with a xylan medium, showed considerable variation in this characteristic.