Miracle-dz/UniFAR-FTUs huggingface dataset:
Can Text-Search Methods of Pathology Reports Accurately Identify Patients with Rectal Cancer in Large Administrative Databases?

Background: The aim of this study is to derive and to validate a cohort of rectal cancer surgical patients within administrative datasets using text-search analysis of pathology reports. Materials and Methods: A text-search algorithm was developed and validated on pathology reports from 694 known rectal cancers, 1000 known colon cancers, and 1000 noncolorectal specimens. The algorithm was applied to all pathology reports available within the Ottawa Hospital Data Warehouse from 1996 to 2010. Identified pathology reports were validated as rectal cancer specimens through manual chart review. Sensitivity, specificity, and positive predictive value (PPV) of the text-search methodology were calculated. Results: In the derivation cohort of pathology reports (n = 2694), the text-search algorithm had a sensitivity and specificity of 100% and 98.6%, respectively. When this algorithm was applied to all pathology reports from 1996 to 2010 (n = 284,032), 5588 pathology reports were identified as consistent with rectal cancer. Medical record review determined that 4550 patients did not have rectal cancer, leaving a final cohort of 1038 rectal cancer patients. Sensitivity and specificity of the text-search algorithm were 100% and 98.4%, respectively. PPV of the algorithm was 18.6%. Conclusions: Text-search methodology is a feasible way to identify all rectal cancer surgery patients through administrative datasets with high sensitivity and specificity. However, in the presence of a low pretest probability, text-search methods must be combined with a validation method, such as manual chart review, to be a viable approach.
Surgical Resection With Radiation Treatment Planning of Spinal Tumors.

BACKGROUND The clinical paradigm for spinal tumors with epidural involvement is challenging considering the rigid dose tolerance of the spinal cord. One effective approach involves open surgery for tumor resection, followed by stereotactic body radiotherapy (SBRT). Resection extent is often determined by the neurosurgeon's clinical expertise, without considering optimal subsequent post-operative SBRT treatment. OBJECTIVE To quantify the effect of incremental epidural disease resection on tumor coverage for spine SBRT in an effort to working towards integrating radiotherapy planning within the operating room. METHODS Ten patients having undergone spinal separation surgery with postoperative SBRT were retrospectively reviewed. Preoperative magnetic resonance imaging was coregistered to postoperative planning computed tomography to delineate the preoperative epidural disease gross tumor volume (GTV). The GTV was digitally shrunk by a series of fixed amounts away from the cord (up to 6 mm) simulating incremental tumor resection and reflecting an optimal dosimetric endpoint. The dosimetric effect on simulated GTVs was analyzed using metrics such as minimum biologically effective dose (BED) to 95% of the simulated GTV (D95) and compared to the unresected epidural GTV. RESULTS Epidural GTV D95 increased at an average rate of 0.88 ± 0.09 Gy10 per mm of resected disease up to the simulated 6 mm limit. Mean BED to D95 was 5.3 Gy10 (31.2%) greater than unresected cases. All metrics showed strong positive correlations with increasing tumor resection margins (R2: 0.989-0.999, P < .01). CONCLUSION Spine separation surgery provides division between the spinal cord and epidural disease, facilitating better disease coverage for subsequent post-operative SBRT. By quantifying the dosimetric advantage prior to surgery on actual clinical cases, targeted surgical planning can be implemented.
Redox imbalance stress in diabetes mellitus: Role of the polyol pathway

In diabetes mellitus, the polyol pathway is highly active and consumes approximately 30% glucose in the body. This pathway contains 2 reactions catalyzed by aldose reductase (AR) and sorbitol dehydrogenase, respectively. AR reduces glucose to sorbitol at the expense of NADPH, while sorbitol dehydrogenase converts sorbitol to fructose at the expense of NAD+, leading to NADH production. Consumption of NADPH, accumulation of sorbitol, and generation of fructose and NADH have all been implicated in the pathogenesis of diabetes and its complications. In this review, the roles of this pathway in NADH/NAD+ redox imbalance stress and oxidative stress in diabetes are highlighted. A potential intervention using nicotinamide riboside to restore redox balance as an approach to fighting diabetes is also discussed.
A Method of Coupling Expected Patch Log Likelihood and Guided Filtering for Image Denoising

With the advent of the information society, image restoration technology has aroused considerable interest. Guided image filtering is more effective in suppressing noise in homogeneous regions, but its edge-preserving property is poor. As such, the critical part of guided filtering lies in the selection of the guided image. The result of the Expected Patch Log Likelihood (EPLL) method maintains a good structure, but it is easy to produce the ladder effect in homogeneous areas. According to the complementarity of EPLL with guided filtering, we propose a method of coupling EPLL and guided filtering for image de-noising. The EPLL model is adopted to construct the guided image for the guided filtering, which can provide better structural information for the guided filtering. Meanwhile, with the secondary smoothing of guided image filtering in image homogenization areas, we can improve the noise suppression effect in those areas while reducing the ladder effect brought about by the EPLL. The experimental results show that it not only retains the excellent performance of EPLL, but also produces better visual effects and a higher peak signal-to-noise ratio by adopting the proposed method.
On the Reproducibility of Psychological Science

ABSTRACT Investigators from a large consortium of scientists recently performed a multi-year study in which they replicated 100 psychology experiments. Although statistically significant results were reported in 97% of the original studies, statistical significance was achieved in only 36% of the replicated studies. This article presents a reanalysis of these data based on a formal statistical model that accounts for publication bias by treating outcomes from unpublished studies as missing data, while simultaneously estimating the distribution of effect sizes for those studies that tested nonnull effects. The resulting model suggests that more than 90% of tests performed in eligible psychology experiments tested negligible effects, and that publication biases based on p-values caused the observed rates of nonreproducibility. The results of this reanalysis provide a compelling argument for both increasing the threshold required for declaring scientific discoveries and for adopting statistical summaries of evidence that account for the high proportion of tested hypotheses that are false. Supplementary materials for this article are available online.
Violencia contra la mujer: rol del ginecólogo en el combate de un flagelo que impacta negativamente en la salud integral de la mujer

Objective: To determine the female sexual function of health workers. Method: quantitative, descriptive, cross-sectional study. The universe is made by women who work in a high complexity hospital, ranging from 20 to 64 years old. The biosociodemographic profile of the worker was characterized by the Female Sexual Function Index (FSFI). Statistical analysis was performed using univariate and bivariate analysis. Pearson or Spearman correlation coefficient was used and analysis of variance was applied. Results: The FSFI score achieved its best around 35-39 years (29.7 ± 4.9) and then it decreases progressively (23.0 ± 8.9). It shows 32.6% of sexual dysfunction, 29% of desire disorder, 10.4% of arousal difficulties, 5.6% of lubrication problems, 9.7% of orgasm disorder, 14% of problems of sexual satisfaction and 9.9% of dyspareunia. Conclusions: The FSFI in health female workers vary in accordance with age, menopause, education and sexual problems in couples. The auxiliary service establishment reached higher rates of sexual dysfunction.
Sistemas de garantía de crédito en América Latina: Orientaciones operativas

El interes de los gobiernos, del sector financiero y del sector empresarial en America Latina y el Caribe por superar los obstaculos al financiamiento que afectan el dinamismo emprendedor de las micro, pequenas y medianas empresas (mipyme) se ha potenciado sustancialmente en los ultimos anos. Nada puede discutirse acerca de la importancia del credito en condiciones razonables (en terminos de volumen, costos y plazos) para el crecimiento competitivo de las mipymes de Latinoamerica y el Caribe, y en especial para el desarrollo de sus economias regionales. Este libro contiene una revision exhaustiva de ocho sistemas de garantia de credito latinoamericanos, distinguiendo entre fondos y sociedades de garantia, ademas de realizar un analisis de los aspectos particulares de cada uno de ellos. Una de las conclusiones mas importantes es la necesidad de obtener pruebas contundentes sobre la adicionalidad crediticia que supuestamente generan estos sistemas --que estaria constatada en el caso de Chile-- como condicion previa para que se apliquen en aquellos paises interesados.
Convergent evolution of tertiary structure in rhodopsin visual proteins from vertebrates and box jellyfish

Significance Complex photoreceptors have independently evolved in animals with radial and bilateral symmetry, but little is known about the proteins that transduce light information (opsins) in radially symmetrical animals. We use homology modeling and heterologous action spectroscopy to study the structure of an opsin (JellyOp) from the lens eye of the visually competent box jellyfish, Carybdea rastonii. We find that a key structural feature of animal opsins—the counterion—maintains visible-light sensitivity in JellyOp from a unique location, E94 in the transmembrane bundle. This unique position for the counterion, the third only discovered in animal opsins, closely mirrors the location in vertebrate visual proteins, which was thought to be a unique adaptation in vertebrates to achieve higher fidelity photoreception. Box jellyfish and vertebrates are separated by >500 million years of evolution yet have structurally analogous lens eyes that employ rhodopsin photopigments for vision. All opsins possess a negatively charged residue—the counterion—to maintain visible-light sensitivity and facilitate photoisomerization of their retinaldehyde chromophore. In vertebrate rhodopsins, the molecular evolution of the counterion position—from a highly conserved distal location in the second extracellular loop (E181) to a proximal location in the third transmembrane helix (E113)—is established as a key driver of higher fidelity photoreception. Here, we use computational biology and heterologous action spectroscopy to determine whether the appearance of the advanced visual apparatus in box jellyfish was also accompanied by changes in the opsin tertiary structure. We found that the counterion in an opsin from the lens eye of the box jellyfish Carybdea rastonii (JellyOp) has also moved to a unique proximal location within the transmembrane bundle—E94 in TM2. Furthermore, we reveal that this Schiff base/counterion system includes an additional positive charge—R186—that has coevolved with E94 to functionally separate E94 and E181 in the chromophore-binding pocket of JellyOp. By engineering this pocket—neutralizing R186 and E94, or swapping E94 with the vertebrate counterion E113—we can recreate versions of the invertebrate and vertebrate counterion systems, respectively, supporting a relatively similar overall architecture in this region of animal opsins. In summary, our data establish the third only counterion site in animal opsins and reveal convergent evolution of tertiary structure in opsins from distantly related species with advanced visual systems.
Practical Application of Domain Dependent Confidence Measurement for Spoken Language Understanding Systems

Spoken Language Understanding (SLU), which extracts semantic information from speech, is not flawless, specially in practical applications. The reliability of the output of an SLU system can be evaluated using a semantic confidence measure. Confidence measures are a solution to improve the quality of spoken dialogue systems, by rejecting low-confidence SLU results. In this study we discuss real-world applications of confidence scoring in a customer service scenario. We build confidence models for three major types of dialogue states that are considered as different domains: how may I help you, number capture, and confirmation. Practical challenges to train domain-dependent confidence models, including data limitations, are discussed, and it is shown that feature engineering plays an important role to improve performance. We explore a wide variety of predictor features based on speech recognition, intent classification, and high-level domain knowledge, and find the combined feature set with the best rejection performance for each application.
Prevalence of Usutu and West Nile virus antibodies in human sera, Modena, Italy, 2012

A collection of 3069 human sera collected in the area of the municipality of Modena, Emilia Romagna, Italy, was retrospectively investigated for specific antibodies against Usutu (USUV) and West Nile viruses (WNV). All the samples resulting positive using a preliminary screening test were analyzed with the plaque reduction neutralization test. Overall, 24 sera were confirmed as positive for USUV (0.78%) and 13 for WNV (0.42%). The results suggest that in 2012, USUV was circulating more than WNV in North‐eastern Italy.
Amelioration of Single Clove Black Garlic Aqueous Extract on Dyslipidemia and Hepatitis in Chronic Carbon Tetrachloride Intoxicated Swiss Albino Mice

Single clove garlic is the product of atypical bulbing process of garlic under specific conditions. Therefore, the number of researches on single clove garlic bioactivity is limited. Recently, the hepatoprotective effect of single clove garlic has been demonstrated. In this study, we investigated amelioration of single clove black garlic aqueous extract, a processed product from single clove garlic, on dyslipidemia and hepatitis induced by chronic administration of CCl4. Mice were randomly divided into four groups: control, extract control, CCl4 intoxication, and coadministrated CCl4 and extract group. Mice were orally given a dose of 1 ml/kg body weight of CCl4 for 28 days twice a week to establish chronic liver injury model. To evaluate the hepatoprotective effect of single clove black garlic, mice were cotreated with CCl4 and single clove black garlic extract (200 mg/kg body weight) via gastric gauge for 30 days. Cotreatment with CCl4 and extract could improve the changes of body weight, liver weight, and relative liver weight as compared to CCl4 intoxicated mice. Single clove black garlic ameliorated dyslipidemia and the elevation of ALT and AST levels induced by chronic CCl4 intoxication. Histological studies revealed that single clove black garlic could prevent mononuclear cells infiltration and hepatocyte necrosis.
KNEE A historical perspective of PCL bracing

Purpose Currently there are many functional knee braces but very few designed to treat the posterior cruciate ligament (PCL). No PCL braces have been biomechanically validated to demonstrate that they provide stability with proper force distribution to the PCL-deficient knee. The purpose of this review was to evaluate the history and current state of PCL bracing and to identify areas where further progress is required to improve patient outcomes and treatment options. Methods A PubMed search was conducted with the terms ‘‘posterior cruciate ligament’’, ‘‘rehabilitation’’, ‘‘history’’, ‘‘knee’’, and ‘‘brace’’, and the relevant articles from 1967 to 2011 were analysed. A review of the current available PCL knee bracing options was performed. Results Little evidence exists from the eight relevant articles to support the biomechanical efficacy of nonoperative and postoperative PCL bracing protocols. Clinical outcomes reported improvements in reducing PCL laxity with anterior directed forces to the tibia during healing following PCL tears. Biomechanics research demonstrates that during knee flexion, the PCL experiences variable tensile forces. One knee brace has been specifically designed and clinically validated to improve stability in PCL-deficient knees during rehabilitation. While available PCL braces demonstrate beneficial patient outcomes, they lack evidence validating their biomechanical effectiveness. Conclusions There is limited information evaluating the specific effectiveness of PCL knee braces. A properly designed PCL brace should apply correct anatomic joint forces that vary with the knee flexion angle and also provide adjustability to satisfy the demands of various activities. No braces are currently available with biomechanical evidence that satisfies these requirements. Level of evidence IV.
Pneumococcal carriage in children and their household contacts six years after introduction of the 13-valent pneumococcal conjugate vaccine in England

Background In April 2010, 13-valent pneumococcal conjugate vaccine (PCV13) replaced PCV7 in the infant immunisation schedule in England and Wales. Despite limited serotype replacement in invasive pneumococcal disease (IPD) during the first four post-PCV13 years, non-vaccine type (NVT) IPD increased substantially in 2014/15. We undertook a carriage study in 2015/16 to help understand the reasons for this increase. Methods and findings Families with a child aged <5 years attending a participating general practice in Gloucestershire or Hertfordshire were invited to provide nasopharyngeal swabs from all consenting members. Swabs from 650 individuals (293 under five, 73 five to twenty and 284 >twenty years) were cultured and serotyped for Streptococcus pneumoniae. Results were compared with those from three previous household studies conducted in the same populations between 2001 to 2013, and with the serotypes causing IPD to estimate case-carrier ratios (CCRs). Overall carriage prevalence did not differ between the four carriage studies with reductions in vaccine-type carriage offset by increases in NVT carriage. While no individual NVT serotype showed an increase in CCR from 2012/13, the composition of the serotypes comprising the NVT group differed such that the overall CCR of the NVT group had significantly increased since 2012/13. Carriage of two PCV13 serotypes, 3 and 19A, was found in 2015/16 (3/650 = 0.5% and 2/650 = 0.3% respectively) with no overall reduction in carriage prevalence of PCV13-7 serotypes since 2012/13, though 6C prevalence, a vaccine-related serotype, had reduced from 1.8% in 2012/13 to 2/648 (0.3%) in 2015/16, p = 0.013. Conclusions There was continuing evolution in carried NVTs six years after PCV13 introduction which, in addition to being vaccine-driven, could also reflect natural secular changes in certain NVTs. This poses challenges in predicting future trends in IPD. Elimination of carriage and disease due to serotypes 3 and 19A may not be achieved by PCV13.
Natural Answer Generation with Heterogeneous Memory

Memory augmented encoder-decoder framework has achieved promising progress for natural language generation tasks. Such frameworks enable a decoder to retrieve from a memory during generation. However, less research has been done to take care of the memory contents from different sources, which are often of heterogeneous formats. In this work, we propose a novel attention mechanism to encourage the decoder to actively interact with the memory by taking its heterogeneity into account. Our solution attends across the generated history and memory to explicitly avoid repetition, and introduce related knowledge to enrich our generated sentences. Experiments on the answer sentence generation task show that our method can effectively explore heterogeneous memory to produce readable and meaningful answer sentences while maintaining high coverage for given answer information.
Using developers' features to estimate story points

Effort estimation is important to correctly plan the use of resources in a software project. In agile projects, a correct effort estimation helps decide which issues have to be fixed or finished during the next iteration. However, estimating issues can be a complex task and developers may make inaccurate estimates. Therefore, the use of automatic approaches that aim to support developers in the estimation process is worth to be studied. We explore the use of a predictive model that use developers' features to assign story points to issue reports. The performance of the model is compared with the performance of models based on features extracted from the text of issues. We assessed the models with different performance metrics including Accuracy, Mean Absolute Error, and Standardized Accuracy. The preliminary results show that the model that uses developers' features sightly outperforms the models based on text features, indicating a promising research direction.
The Evolving Role of Rituximab in Adult Minimal Change Glomerulopathy

Background: Minimal-change glomerulopathy is defined histologically by the presence of normal glomeruli on light microscopy and diffuse podocyte effacement on electron microscopy. Although effective in children, corticosteroid treatment in adults is more variable and time to response can be prolonged. Data to support rituximab use in adults with corticosteroid-dependent or resistant minimal-change glomerulopathy are limited. Here, we describe the clinical course of adults with corticosteroid-dependent or -resistant minimal-change glomerulopathy who received rituximab. Methods: Demographic and clinical data were collected and analyzed from all adult patients with native kidney, biopsy-proven, minimal-change glomerulopathy who were administered rituximab between 2009 and 2014 and cared for at the UNC Kidney Center. Results: Ten patients with corticosteroid-resistant (n = 5) or corticosteroid-dependent (n = 5) idiopathic minimal-change glomerulopathy were treated with rituximab between 2009 and 2014. Rituximab treatment induced remission in all 10 patients with a median time to remission of 2 months. The median time from rituximab to corticosteroid discontinuation was 3.5 months. The median remission time was 29 months and follow-up time was 39.5 months. No serious adverse events attributable to rituximab were observed. Conclusion: Rituximab induced remission in all patients with corticosteroid-dependent or -resistant minimal-change glomerulopathy, and may hold great therapeutic potential with good efficacy and minimal toxicity. Mounting evidence implies that a well-conducted randomized controlled clinical trial using rituximab in adults with minimal-change glomerulopathy in both corticosteroid-resistant and corticosteroid-dependent patients is warranted.