Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyclic histological changes of the oviductal‐cloacal junction in the viviparous snake Toluca lineata

The structure and seasonal changes of the oviductal‐cloacal junction remain poorly understood in most squamates. This study was undertaken to describe the histology of the oviductal‐cloaca junction of a female viviparous snake Toluca lineata, during gestation, previtellogenesis, and vitellogenesis. The oviductal‐cloacal junction exhibits a wider lumen and thicker layers of connective tissue, smooth muscle layers, and total wall width compared to the posterior vagina. The lining is characterized by thick, short longitudinal mucosal folds. The luminal epithelia differ morphologically from anterior to posterior portions of the oviductal‐cloacal junction. The anterior portion is lined with a simple columnar epithelium composed of nonciliated cells. The middle portion is lined with stratified epithelium that contains an apical columnar cell layer that undergoes morphological changes coincident with the reproductive cycle. The posterior portion is lined with a stratified squamous epithelium. The connective tissue underlying the epithelium contains numerous ovoid cells having abundant acidophilic cytoplasmic granules—eosinophils. Copulation occurs during the previtellogenic stage, as evidenced by the presence of abundant spermatozoa in the lumen of the anterior portion and of a copulatory plug in the middle and posterior portion of the oviductal‐cloacal junction. J. Morphol. 237:91–100, 1998. © 1998 Wiley‐Liss, Inc.
HIV, HCV, HBV, and syphilis among transgender women from Brazil

Abstract Different sampling strategies, analytic alternatives, and estimators have been proposed to better assess the characteristics of different hard-to-reach populations and their respective infection rates (as well as their sociodemographic characteristics, associated harms, and needs) in the context of studies based on respondent-driven sampling (RDS). Despite several methodological advances and hundreds of empirical studies implemented worldwide, some inchoate findings and methodological challenges remain. The in-depth assessment of the local structure of networks and the performance of the available estimators are particularly relevant when the target populations are sparse and highly stigmatized. In such populations, bottlenecks as well as other sources of biases (for instance, due to homophily and/or too sparse or fragmented groups of individuals) may be frequent, affecting the estimates. In the present study, data were derived from a cross-sectional, multicity RDS study, carried out in 12 Brazilian cities with transgender women (TGW). Overall, infection rates for HIV and syphilis were very high, with some variation between different cities. Notwithstanding, findings are of great concern, considering the fact that female TGW are not only very hard-to-reach but also face deeply-entrenched prejudice and have been out of the reach of most therapeutic and preventive programs and projects. We cross-compared findings adjusted using 2 estimators (the classic estimator usually known as estimator II, originally proposed by Volz and Heckathorn) and a brand new strategy to adjust data generated by RDS, partially based on Bayesian statistics, called for the sake of this paper, the RDS-B estimator. Adjusted prevalence was cross-compared with estimates generated by non-weighted analyses, using what has been called by us a naïve estimator or rough estimates.
Towards Qualitative Word Embeddings Evaluation: Measuring Neighbors Variation

We propose a method to study the variation lying between different word embeddings models trained with different parameters. We explore the variation between models trained with only one varying parameter by observing the distributional neighbors variation and show how changing only one parameter can have a massive impact on a given semantic space. We show that the variation is not affecting all words of the semantic space equally. Variation is influenced by parameters such as setting a parameter to its minimum or maximum value but it also depends on the corpus intrinsic features such as the frequency of a word. We identify semantic classes of words remaining stable across the models trained and specific words having high variation.
Father Involvement and Firstborn Adjustment to the Birth of a Sibling

The relationship between fathers’ involvement with child care and firstborns’ adjustment to the birth of a sibling was examined in a sample of 225 families participating in a longitudinal investigation of changes following the birth of a second child. Firstborn adjustment was assessed using five scales: sleep problems, separation anxiety, opposition, emotional distress, and toileting accidents. Results revealed significant increases from prenatal to 1 month for opposition and emotional distress for mothers and fathers, and decreases in separation anxiety for mothers and toileting accidents for fathers. Parents reported more opposition for boys and more separation anxiety for girls. Father involvement had an effect on firstborns’ separation anxiety and emotional distress. These results highlight the importance of fathers’ involvement in firstborns’ adjustment in protecting against problematic emotional adjustment during the transition to siblinghood.
Network meta-analysis, a new statistical technique at urologists' disposal to improve decision making

Structured summary Provide a structured summary including, as applicable: Background: main objectives Methods: data sources; study eligibility criteria, participants, and interventions; study appraisal; and synthesis methods, such as network meta-analysis. Results: number of studies and participants identified; summary estimates with corresponding confidence/credible intervals; treatment rankings may also be discussed. Authors may choose to summarize pairwise comparisons against a chosen treatment included in their analyses for brevity. Discussion/Conclusions: limitations; conclusions and implications of findings. Others: primary source of funding; systematic review registration number with registry name.
Performance Evaluation of the Preanalytic Module of the ACL TOP 750 Hemostasis Lab System

Dear Editor, Hemolysis, icterus, and lipemia are important preanalytic sources of errors in coagulation testing of blood samples, besides sample-to-anticoagulant ratio, transport stability, and storage temperature. Lipemia (13%), hyperbilirubinemia (11%), and hemolysis (4%) in whole blood cause errors in coagulation testing [1, 2]. Hemoglobin, bilirubin, and triglyceride are major interfering substances that affect test results by spectral overlap [3, 4]. Hemolytic, icteric, and lipemic (HIL) sample check functions have been implemented in the preanalytic module of the ACL TOP family 50 series spectrophotometric hemostasis equipment (Instrumentation Laboratory Company, Bedford, MA, USA) to support preanalytic sample evaluation. We evaluated the performance of the ACL TOP 750 preanalytic module, using patient samples. In total, 353 blood samples assigned HIL flags by the ACL TOP 750 preanalytic module were collected from samples subjected to the routine hemostasis test. HIL sample flags were given based on absorbance at a specific wavelength. Samples were collected between June and September 2016 and in August 2017 at Gachon University Gil Medical Center, Korea. There were 80 samples with hemolysis flag, 185 samples with icteric flag, 33 samples with lipemic flag, and 55 samples from patients with triglyceride levels over 5,000 mg/L, including samples without lipemic flag. Preanalytic values measured by the ACL TOP 750 preanalytic module were compared with reference values obtained from ADVIA chemistry XPT (Siemens Healthineers, Erlangen, Germany) using an enzymatic method and from ADVIA 2120i (Siemens Healthineers, Erlangen, Germany) using a spectrophotometric method. Medians of preanalytic readings were used for analysis. Passing–Bablok regression and Bland–Altman tests were conducted for hemolytic and icteric sample evaluation. Linear regression analysis was conducted for lipemic samples. In each HIL sample group, subgroups of samples with HIL flag and with a value interval around the modal value of the reference method, which included 68% of all samples with 95% confidence level, were defined as low-level HIL samples (Table 1). Passing–Bablok regression for hemolytic samples revealed constant, non-proportional differences between reference and preanalytic values (Fig. 1A). In a Bland–Altman plot, 77/80 (96.3%) hemolytic and 55/58 (94.8%) low-level hemolytic samples were within the limit of agreement (Fig. 1B, 1C). For icteric samples, Passing–Bablok regression indicated constant, proportional differences between reference and preanalytic values (Fig. 1D). In a Bland–Altman plot, 174/185 (94.1%) icteric and 127/137 (92.7%) low-level icteric samples were within the limit of agreement (Fig. 1E, 1F). The CUSUM test for linearity, indi-
Use of the critical-care pain observation tool and the bispectral index for the detection of pain in brain-injured patients undergoing mechanical ventilation

Abstract The assessment of pain in patients with brain injury is challenging due to impaired ability to communicate. We aimed to test the reliability and validity of the critical-care pain observation tool (CPOT) and the bispectral index (BIS) for pain detection in critically brain-injured patients. This prospective observational study was conducted in a neurosurgical intensive care unit in a University-Affiliated Hospital. Adult brain-injured patients undergoing mechanical ventilation were enrolled. Nociceptive (endotracheal suctioning) and non-nociceptive (gentle touching) procedures were performed in a random crossover fashion. Before and immediately after the procedure, CPOT was evaluated by 2 residents and 2 chief nurses, and BIS was documented. The ability to self-report pain was also assessed. The inter-observer reliability of CPOT was analyzed. The criterion and discriminant validities of the CPOT and the BIS were tested. During the study, we enrolled 400 brain-injured patients. The ability to self-report pain was maintained in 214 (54%) and 218 (55%) patients during suctioning and gentle touching, respectively. The intraclass correlation coefficients (95% confidence interval) for inter-observer reliability of CPOT ranged from 0.86 (0.83–0.89) to 0.93 (0.91–0.94). Using self-reported pain as the reference, the area under the receiver operating characteristic curve (95% confidence interval) was 0.84 (0.80–0.88) for CPOT and 0.76 (0.72–0.81) for BIS. When the 2 instruments were combined as either CPOT ≥2 or BIS ≥88 after the procedure, the sensitivity and specificity were 0.90 (0.85–0.93) and 0.59 (0.52–0.66), respectively; and when the 2 instruments were combined as both CPOT ≥2 and BIS ≥88, the sensitivity and specificity were 0.62 (0.55—0.68) and 0.89 (0.83–0.93). Both CPOT and BIS increased significantly after suctioning (all P < .001) but remained unchanged after gentle touching (P ranging from .06 to .14). Our criterion and discriminant validity results supported the use of CPOT and BIS to detect pain in critically brain-injured patients. Combining use of CPOT and BIS in different ways might provide comprehensive pain assessment for different purposes.
How tobacco companies have used package quantity for consumer targeting

Introduction Package quantity refers to the number of cigarettes or amount of other tobacco product in a package. Many countries restrict minimum cigarette package quantities to avoid low-cost packs that may lower barriers to youth smoking. Methods We reviewed Truth Tobacco Industry Documents to understand tobacco companies’ rationales for introducing new package quantities, including companies’ expectations and research regarding how package quantity may influence consumer behaviour. A snowball sampling method (phase 1), a static search string (phase 2) and a follow-up snowball search (phase 3) identified 216 documents, mostly from the 1980s and 1990s, concerning cigarettes (200), roll-your-own tobacco (9), smokeless tobacco (6) and ‘smokeless cigarettes’ (1). Results Companies introduced small and large packages to motivate brand-switching and continued use among current users when faced with low market share or threats such as tax-induced price increases or competitors’ use of price promotions. Companies developed and evaluated package quantities for specific brands and consumer segments. Large packages offered value-for-money and matched long-term, heavy users’ consumption rates. Small packages were cheaper, matched consumption rates of newer and lighter users, and increased products’ novelty, ease of carrying and perceived freshness. Some users also preferred small packages as a way to try to limit consumption or quit. Conclusion Industry documents speculated about many potential effects of package quantity on appeal and use, depending on brand and consumer segment. The search was non-exhaustive, and we could not assess the quality of much of the research or other information on which the documents relied.
Development of a micromanipulation method for single cell isolation of prokaryotes and its application in food safety

For nearly a century, conventional microbiological methods have been standard practice for detecting and identifying pathogens in food. Nevertheless, the microbiological safety of food has improved and various rapid methods have been developed to overcome the limitations of conventional methods. Alternative methods are expected to detect low cell numbers, since the presence in food of even a single cell of a pathogenic organism may be infectious. With respect to low population levels, the performance of a detection method is assessed by producing serial dilutions of a pure bacterial suspension to inoculate representative food matrices with highly diluted bacterial cells (fewer than 10 CFU/ml). The accuracy of data obtained by multiple dilution techniques is not certain and does not exclude some colonies arising from clumps of cells. Micromanipulation techniques to capture and isolate single cells from environmental samples were introduced more than 40 years ago. The main limitation of the current micromanipulation technique is still the low recovery rate for the growth of a single cell in culture medium. In this study, we describe a new single cell isolation method and demonstrate that it can be used successfully to grow various types of microorganism from picked individual cells. Tests with Gram-positive and Gram-negative organisms, including cocci, rods, aerobes, anaerobes, yeasts and molds showed growth recovery rates from 60% to 100% after micromanipulation. We also highlight the use of our method to evaluate and challenge the detection limits of standard detection methods in food samples contaminated by a single cell of Salmonella enterica.
Simulation of dual carbon–bromine stable isotope fractionation during 1,2-dibromoethane degradation*

ABSTRACT We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon–bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.
L‐PRF for increasing the width of keratinized mucosa around implants: A split‐mouth, randomized, controlled pilot clinical trial

BACKGROUND This study aims to evaluate the use of the leukocyte- and platelet-rich fibrin (L-PRF) membranes in increasing the width of the keratinized mucosa (KM) around implants. MATERIAL AND METHODS Eight patients in need for bilateral widening of the KM around implants in the lower jaw were recruited for a spit-mouth randomized controlled trial. At the control site, a free gingival graft (FGG) was used, whereas at the other side (test), L-PRF membranes were applied. The primary outcome was the increase in width of KM around the implants. As secondary outcomes, the postoperative pain and surgical time were assessed. The follow-up period was 6 weeks. RESULTS A significant increase in the total bucco-lingual width of KM in both groups was observed, with 1.3 mm ± 0.9 extra gain (P < .05) for the FGG sites. Shrinkage of the widened areas in this period was 32.1% at the test site and 23.6% at the control site. All values of the postoperative pain scores at the control site were higher than at the test site. The mean surgery time in the test and control group was 29.1 ± 4.8 and 48.1 ± 7.7 minutes, respectively. CONCLUSION Within the limitations of this randomized controlled trial with split mouth design, it can be concluded that L-PRF can increase the width of KM around implants. Furthermore, the use of L-PRF results in a lower surgical time with less postoperative discomfort and pain for the patients in comparison to the FGG.
Endoscopic Ultrasound-Guided Gallbladder Drainage Using a Lumen-Apposing Metal Stent for Acute Cholecystitis: A Systematic Review

Surgery remains the standard treatment for acute cholecystitis except in high-risk candidates where percutaneous transhepatic gallbladder drainage (PT-GBD), endoscopic transpapillary cystic duct stenting (ET-CDS), and endoscopic ultrasound-guided gallbladder drainage (EUS-GBD) are potential choices. PT-GBD is contraindicated in patients with coagulopathy or ascites and is not preferred by patients owing to aesthetic reasons. ET-CDS is successful only if the cystic duct can be visualized and cannulated. For 189 patients who underwent EUS-GBD via insertion of a lumen-apposing metal stent (LAMS), the composite technical success rate was 95.2%, which increased to 96.8% when LAMS was combined with co-axial self-expandable metal stent (SEMS). The composite clinical success rate was 96.7%. We observed a small risk of recurrent cholecystitis (5.1%), gastrointestinal bleeding (2.6%) and stent migration (1.1%). Cautery enhanced LAMS significantly decreases the stent deployment time compared to non-cautery enhanced LAMS. Prophylactic placement of a pigtail stent or SEMS through the LAMS avoids re-interventions, particularly in patients, where it is intended to remain in situ indefinitely. Limited evidence suggests that the efficacy of EUS-GBD via LAMS is comparable to that of PT-GBD with the former showing better results in postoperative pain, length of hospitalization, and need for antibiotics. EUS-GBD via LAMS is a safe and efficacious option when performed by experts.
The third ventricle of the human fetal brain: Normative data and pathologic correlation. A 3D transvaginal neurosonography study

The objective of the study are to describe (a) the technical aspects and (b) the anatomical boundaries of the fetal third ventricle (3V) on the midsagittal sonographic view and to assess (c) different biometric parameters in normal and abnormal fetuses and (d) and their reproducibility.
The Outcome of the Cryptococcus neoformans–Macrophage Interaction Depends on Phagolysosomal Membrane Integrity

Cryptococcus neoformans is a fungal pathogen with worldwide distribution. C. neoformans resides within mature phagolysosomes where it often evades killing and replicates. C. neoformans induces phagolysosomal membrane permeabilization (PMP), but the mechanism for this phenomenon and its consequences for macrophage viability are unknown. In this study, we used flow cytometry methodology in combination with cell viability markers and LysoTracker to measure PMP in J774.16 and murine bone marrow–derived macrophages infected with C. neoformans. Our results showed that cells manifesting PMP were positive for apoptotic markers, indicating an association between PMP and apoptosis. We investigated the role of phospholipase B1 in C. neoformans induction of PMP. Macrophages infected with a C. neoformans Δplb1 mutant had reduced PMP compared with those infected with wild-type and phospholipase B1–complemented strains, suggesting a mechanism of action for this virulence factor. Capsular enlargement inside macrophages was identified as an additional likely mechanism for phagolysosomal membrane damage. Macrophages undergoing apoptosis did not maintain an acidic phagolysosomal pH. Induction of PMP with ciprofloxacin enhanced macrophages to trigger lytic exocytosis whereas nonlytic exocytosis was common in those without PMP. Our results suggest that modulation of PMP is a critical event in determining the outcome of C. neoformans–macrophage interaction.
Modeling the Heterogeneity of Dengue Transmission in a City

Dengue fever is one of the most important vector-borne diseases in the world, and modeling its transmission dynamics allows for determining the key influence factors and helps to perform interventions. The heterogeneity of mosquito bites of humans during the spread of dengue virus is an important factor that should be considered when modeling the dynamics. However, traditional models generally assumed homogeneous mixing between humans and vectors, which is inconsistent with reality. In this study, we proposed a compartmental model with negative binomial distribution transmission terms to model this heterogeneity at the population level. By including the aquatic stage of mosquitoes and incorporating the impacts of the environment and climate factors, an extended model was used to simulate the 2014 dengue outbreak in Guangzhou, China, and to simulate the spread of dengue in different scenarios. The results showed that a high level of heterogeneity can result in a small peak size in an outbreak. As the level of heterogeneity decreases, the transmission dynamics approximate the dynamics predicted by the corresponding homogeneous mixing model. The simulation results from different scenarios showed that performing interventions early and decreasing the carrying capacity for mosquitoes are necessary for preventing and controlling dengue epidemics. This study contributes to a better understanding of the impact of heterogeneity during the spread of dengue virus.