Miracle-dz/UniFAR-FTUs huggingface dataset:
The neutrophil to albumin ratio as a predictor of pathological complete response in rectal cancer patients following neoadjuvant chemoradiation

Pathological complete response (pCR) following neoadjuvant chemoradiotherapy (nCRT) and total mesorectal excision (TME), in patients with locally advanced rectal cancer, occurs in 15–27% of patients. Because blood cell counts and albumin are a direct indicator of the host environment, a response to nCRT might be predicted by these markers. This study was carried out to determine whether the neutrophil to albumin ratio (NAR) was predictive of pCR in veteran patients. Ninety-eight patients with rectal cancer who underwent standard nCRT, followed by TME were analyzed. Pre-nCRT and post-nCRT hematologic data were collected. Univariate and multivariate analyses were carried out. Kaplan–Meier curves were constructed with our primary endpoint of pCR. Male patients (99%), age 62.4±9.1 years, BMI=27.4±5.9 kg/m2, rectal cancer distance from anal verge=7.1±4.5 cm (SD), interval between nCRT and TME=8 weeks, 55% patients=low anterior resection, 95% received 5-fluorouracil, and all patients received radiation, with 15% achieving a pCR. Univariate analysis showed that pre-nCRT carcinoembryonic antigen (15.8±45.1 vs. 3.5±5.3 ng/dl; P=0.002) and the pre-nCRT NAR (16.4±4.8 vs. 14.2±1.6; P=0.002) were associated with pCR. On multivariate analysis, pre-nCRT carcinoembryonic antigen (odds ratio=0.41, 95% confidence interval 0.22–0.77) and pre-nCRT NAR (odds ratio=0.76, 95% confidence interval 0.60–0.97) remained independent predictors of pCR. Overall survival between nonresponders and pCR patients at 1, 5, and 10 years was 96, 62, and 44% versus 93, 85, and 61%, P=0.13, and disease-free survival was 95, 60, and 47% versus 93, 85, and 61%, P=0.17; respectively. Our study shows that the pre-nCRT NAR is an independent predictor of pCR. These findings should be applied to other cohorts to determine its validity and reliability for use as a potential predictor of pCR.
ON PARAMETRIZATION OF THE q-BERNSTEIN BASIS FUNCTIONS AND THEIR APPLICATIONS

In order to investigate the fundamental properties of q-Bernstein basis functions, we give generating functions for these basis functions and their functional and differential equations. In [16], [15] and [17], we construct a novel collection of generating functions to derive many known and some new identities for the classical Bernstein basis functions. The main purpose of this paper is to construct analogous generating functions for the q-Bernstein basis functions. By using an approach similar to that of our methods in [16] as well as some properties of interpolation functions, we can derive some known and some new identities, relations and formulas for the q-Bernstein basis functions, including the partition of unity property, formulas for representing the monomials, recurrence relations, formulas for derivatives, subdivision identities and integral representations. Furthermore, we give plots of not only our new basis functions, but also their generating functions. Also, we simulate q-Bezier type curves for some selected q values and control points.
Performance of QuantiFERON-TB Gold and tuberculin skin test relative to subjects' risk of exposure to tuberculosis.

BACKGROUND Performance of QuantiFERON-TB Gold In-Tube (QFT-GIT) and tuberculin skin test (TST) has not been compared in a US college population with varying risk of tuberculosis exposure. METHODS We performed a retrospective chart review of students tested for tuberculosis at the University of Pennsylvania Student Health Service between 2009 and 2011. We stratified students into high-, low-, and no-risk categories for exposure to tuberculosis and compared QFT-GIT and TST performance in risk groups adjusting demographic characteristics. RESULTS During the study period, 15 936 tuberculosis tests were performed in 9483 college students. Coming from a tuberculosis-endemic country was the only risk factor significantly associated with having a positive result (odds ratio [OR] 12.9; 95% confidence interval [CI], 10.2-16.5). Test specificity was higher for TST than QFT-GIT (99.7% vs 91.4%; P < .0001). Application of a higher threshold for positivity improved comparability of QFT-GIT with TST in the low-risk group (adjusted OR [AOR] 1.2; 95% CI, .4-3.3) but not in the high-risk group (AOR .4; 95% CI, .3-.5). CONCLUSIONS QFT-GIT was less specific than TST. Our findings support the use of TST for US college students who need tuberculosis testing and the use of risk-stratified interpretation for students who are tested with QFT-GIT.
Structural insights into simocyclinone as an antibiotic, effector ligand and substrate

Abstract Simocyclinones are antibiotics produced by Streptomyces and Kitasatospora species that inhibit the validated drug target DNA gyrase in a unique way, and they are thus of therapeutic interest. Structural approaches have revealed their mode of action, the inducible-efflux mechanism in the producing organism, and given insight into one step in their biosynthesis. The crystal structures of simocyclinones bound to their target (gyrase), the transcriptional repressor SimR and the biosynthetic enzyme SimC7 reveal fascinating insight into how molecular recognition is achieved with these three unrelated proteins.
What artifice can and cannot tell us about animal behavior

Abstract Artifice—the manipulation of social and environmental stimuli—is fundamental to research in animal behavior. State-of-the-art techniques have been developed to generate and present complex visual stimuli. These techniques have unique strengths and limitations. However, many of the issues with synthetic animation and virtual reality are common to playback experiments in general, including those using unmanipulated video or auditory stimuli. Playback experiments, in turn, fall into the broader category of experiments that artificially manipulate the array of stimuli experienced by a subject. We argue that the challenges of designing and interpreting experiments using virtual reality or synthetic animations are largely comparable to those of studies using older technologies or addressing other modalities, and that technology alone is unlikely to solve these challenges. We suggest that appropriate experimental designs are the key to validating behavioral responses to artificial stimuli and to interpreting all studies using artifice, including those that present complex visual displays.
Phenotypic profile of Rh blood group systems among females of child-bearing age in Pakistan

The Rh blood group system discovered in 1939 is only second in importance to the ABO system in terms of transfusion [1]. It is a highly complex blood group system with more than fifty different antigens [2]. However, most clinical transfusion issues are associated with the five principal antigens D, C, c, E and e. Rh antigens are non-glycosylated proteins in the RBC membrane [3]. Two closely linked genes on chromosome 1 control the expression of Rh; one gene RhD codes for the presence of RhD, and a second gene codes for the expression of CcEe antigens [4]. The Rh antigens are thought to play a role in maintaining the integrity of the RBC membrane. They may also be involved in transport of ammonium across the RBC membrane [5].
Multi-oriented Scene Text Detection via Corner Localization and Region Segmentation

Previous deep learning based state-of-the-art scene text detection methods can be roughly classified into two categories. The first category treats scene text as a type of general objects and follows general object detection paradigm to localize scene text by regressing the text box locations, but troubled by the arbitrary-orientation and large aspect ratios of scene text. The second one segments text regions directly, but mostly needs complex post processing. In this paper, we present a method that combines the ideas of the two types of methods while avoiding their shortcomings. We propose to detect scene text by localizing corner points of text bounding boxes and segmenting text regions in relative positions. In inference stage, candidate boxes are generated by sampling and grouping corner points, which are further scored by segmentation maps and suppressed by NMS. Compared with previous methods, our method can handle long oriented text naturally and doesn't need complex post processing. The experiments on ICDAR2013, ICDAR2015, MSRA-TD500, MLT and COCO-Text demonstrate that the proposed algorithm achieves better or comparable results in both accuracy and efficiency. Based on VGG16, it achieves an F-measure of 84.3% on ICDAR2015 and 81.5% on MSRA-TD500.
Contextual Variability and Exemplar Strength in Phonotactic Learning

Phonotactics—constraints on the position and combination of speech sounds within syllables—are subject to statistical differences that gradiently affect speaker and listener behavior (e.g., Vitevitch & Luce, 1999). What statistical properties drive the acquisition of such constraints? Because they are naturally highly correlated, previous work has been unable to dissociate the contribution of 2 properties: contextual variability (the number of unique phonological contexts in which a phonotactic pattern appears) and exemplar strength (the overall number of times the pattern appears). Using an artificial language learning paradigm, 3 experiments disentangled the effects of variability and strength, indexed by type and token frequency, respectively, on the learning of gradient phonotactics. When the 2 factors were decorrelated (Experiment 2), participants showed greater generalization of patterns advantaged for contextual variability, but not those advantaged for exemplar strength. When the 2 factors were anticorrelated (Experiment 3), participants preferred patterns advantaged in contextual variability, even though they were disadvantaged for exemplar strength. These results suggest that contextual variability is the key force driving phonotactic learning, as it allows learners to home in on the invariant features of the input.
Oxidative Stress and Antioxidative Status in the Acute Pancreatitis

Acute pancreatitis is the inflammatory condition of a gland, including an invasion into, to a lesser or greater extent, the surrounding tissues, and also the contiguous or distant organs (Braganza, 2001; Frossard et al., 2008). The analysis of the processes, occurring in the course of acute pancreatitis, has made it possible to define this disease as the one which comprises of two phases. Initially, the hyperstimulation of the immunological system with the excessive local activation of the cells of inflammatory focus in the pancreas occurs, and later on, as a result, the systemic response, expressed as Systemic Inflammatory Response Syndrome (SIRS), develops. Compensatory Anti-inflammatory Response Syndrome (CARS) causes early organic complications (Gamaste, 1994; Toouli et al., 2002; Yousaf & McCallion, 2003). The intensification of an inflammatory response, hypoxia and the occurrence of oligovolemic shock may result in the clinical development of Multi-Organ Dysfunction Syndrome (MODS), which is defined as the more advanced stage of SIRS. In this period, greater susceptibility to bacterial infections and fungal infections and, consequently, an increased mortality rate, caused by blood poisoning, is observed. Multi-Organ Dysfunction Syndrome requires the application of the powerful methods of supporting the organism of a patient (Song et al., 2003). Acute pancreatitis is a disease of an unpredictable course. It is, usually, a reversible process, in which the pain ailments of the abdomen undergo regression and the activity of pancreatic enzymes returns to its normal level. In 70 75% of cases, this process becomes subjected to the self-limitation and has the properties of interstitial inflammation. However, in 5 – 15%, a form characterized by severe, necrotic course may develop. In this case, local complications and multi-organic complications are alike present The morbidity rate in case of acute pancreatitis in Poland is estimated to be at the level of 240 cases per 1 million in a year. The mortality rate amounts to 5 10% in total. However, in the cases of severe course, it amounts to approximately 35% (Baillie, 1997; Balthazar et al., 2002; Beger et al., 1997; Lund
A Clustering Approach for Real-Time Control of Queue Spillbacks on Signalized Arterials

When demand exceeds capacity at signalized intersections, queues fail to clear during the allocated green times. This creates oversaturated traffic conditions and when queues reach the upstream intersection a queue spillback occurs that reduces the upstream link capacity in arterials. To mitigate the negative impacts of spillbacks, this paper presents a traffic signal methodology for global management of long queues along signalized arterials. The key idea of the proposed methodology is to implement a real-time partitioning of the arterial to detect critical group(s) of consecutive links with oversaturated traffic conditions. The clustering approach enables to develop locally smaller-sized decentralized signal control strategies operating on the most upstream and downstream intersections of the critical group, with respect to the empty space available in the congested links beyond the back of queue. Simulation investigations on a real-world arterial site demonstrate the benefits of this new approach compared to an existing pre-timed signal control strategy and a classical decentralized green extension strategy.
DRG1 is a potential oncogene in lung adenocarcinoma and promotes tumor progression via spindle checkpoint signaling regulation

Developmentally regulated GTP binding protein 1 (DRG1), a member of the DRG family, plays important roles in regulating cell growth. However, the molecular basis of DRG1 in cell proliferation regulation and the relationship between DRG1 and tumor progression remain poorly understood. Here, we demonstrate that DRG1 is elevated in lung adenocarcinomas while weakly expressed in adjacent lung tissues. DRG1 knockdown causes growth inhibition of tumor cells by significantly increasing the proportion of cells in M phase. Overexpression of DRG1 leads to chromosome missegregation which is an important index for tumorigenesis. Interestingly, ectopic of DRG1 reduces taxol induced apoptosis of lung adenocarcinoma cells. Mechanistic analyses confirm that DRG1 localizes at mitotic spindles in dividing cells and binds to spindle checkpoint signaling proteins in vivo. These studies highlight the expanding role of DRG1 in tumorigenesis and reveal a mechanism of DRG1 in taxol resistance.
Sustained immune tolerance induction in enzyme replacement therapy-treated CRIM-negative patients with infantile Pompe disease.

BACKGROUND Cross-reactive immunological material-negative (CRIM-negative) infantile Pompe disease (IPD) patients develop an immune response against enzyme replacement therapy (ERT) with alglucosidase alfa that nullifies ERT efficacy. Prophylactic immune tolerance induction (ITI) with rituximab, methotrexate, and IVIG successfully prevents development of deleterious rhGAA IgG antibodies; however, safety, likelihood of success, and long-term efficacy of ITI in a larger cohort remain unknown. METHODS Clinical data were analyzed for 19 CRIM-negative IPD patients who received ITI with rituximab, methotrexate, and IVIG in the ERT-naive setting (ERT+ITI) and compared to a historical cohort of 10 CRIM-negative IPD patients on ERT monotherapy. RESULTS ITI was safely tolerated, although infections were reported in 4 patients. Fourteen (74%) ERT+ITI patients were alive, with a median age of 44.2 months at their final assessment. The eldest survivor was 103.9 months old, with 100.2 months of follow-up after initiation of ERT+ITI. Death (n = 5) occurred at a median age of 29.2 months and was unrelated to the administration of ITI. Fifteen patients either did not seroconvert (n = 8) or maintained low titers (n = 7; defined as titers of ≤6,400 throughout the course of ERT) following ERT+ITI. Only one patient developed high and sustained antibody titers (defined as titers of ≥51,200 at or beyond 6 months on ERT). Left ventricular mass index (LVMI) decreased from a median of 248.5 g/m2 at baseline to 76.8 g/m2 at a median time from ERT+ITI initiation to 59 weeks. ERT+ITI significantly improved overall survival (P = 0.001), eliminated/reduced antibodies at values of ≤6,400 at week 52 on ERT (P = 0.0004), and improved LVMI at week 52 on ERT (P = 0.02) when compared with ERT monotherapy. CONCLUSION Evidence from this international cohort of CRIM-negative IPD patients further supports the safety, feasibility, and efficacy of ITI in the prevention of immune responses to ERT. TRIAL REGISTRATION Clinicaltrials.gov NCT01665326. FUNDING This research was supported in part by the Lysosomal Disease Network, a part of NIH Rare Diseases Clinical Research Network, and by a grant from Genzyme, a Sanofi company.
The influence of KIR gene presence/absence polymorphisms on the development of periodontal disease in smokers and non-smokers

Introduction Periodontal diseases are highly prevalent inflammatory, multifactorial diseases. Smoking is one of the most important environmental risk factors for the development and severity of periodontal disease. Killer cell immunoglobulin-like receptors (KIRs) are members of the immunoglobulin (Ig) superfamily and play an essential role in the regulation of NK cell activity, allowing natural killer (NK) cells to sense and respond to human leukocyte antigen (HLA) class I. The aim of this study was to evaluate the influence of KIR gene presence/absence polymorphisms on the development of periodontal disease in smokers and non-smokers. Material and methods This study enrolled 400 Caucasian subjects (age range 25-69 years) from the West Pomeranian region of Poland. The subjects were categorized into four subgroups (smoking and non-smoking patients with periodontal disease; smoking and non-smoking subjects without periodontal disease – control subjects). Results The differences of KIR gene frequencies between non-smoking patients and non-smoking control subjects as well as smoking patients and control subjects were not statistically significant. In multivariate regression analysis advanced age of patients and smoking were independent factors associated with increased frequency of periodontal disease. Conclusions The results of this study suggest that the main factor associated with increased risk of periodontal disease is smoking, whereas KIR presence/absence polymorphism is not a significant factor involved in the pathogenesis of periodontal disease.
Rigidity of crystalline color superconducting quark matter

We calculate the shear modulus of crystalline color superconducting quark matter, showing that this phase of dense, but not asymptotically dense, three-flavor quark matter responds to shear stress like a very rigid solid. To evaluate the shear modulus, we derive the low-energy effective Lagrangian that describes the phonons that originate from the spontaneous breaking of translation invariance by the spatial modulation of the gap parameter {delta}. These massless bosons describe space- and time-dependent fluctuations of the crystal structure and are analogous to the phonons in ordinary crystals. The coefficients of the spatial derivative terms of the phonon effective Lagrangian are related to the elastic moduli of the crystal; the coefficients that encode the linear response of the crystal to a shearing stress define the shear modulus. We analyze the two particular crystal structures which are energetically favored over a wide range of densities, in each case evaluating the phonon effective action and the shear modulus up to order {delta}{sup 2} in a Ginzburg-Landau expansion, finding shear moduli which are 20 to 1000 times larger than those of neutron star crusts. The crystalline color superconducting phase has long been known to be a superfluid--by picking a phase its order parameter breaksmore » the quark-number U(1){sub B} symmetry spontaneously. Our results demonstrate that this superfluid phase of matter is at the same time a rigid solid. We close with a rough estimate of the pinning force on the rotational vortices which would be formed embedded within this rigid superfluid upon rotation. Our results raise the possibility that (some) pulsar glitches could originate within a quark matter core deep within a neutron star. « less
Analysis of abstracts presented at the prosthodontic research section of IADR General Sessions 2004-2005: demographics, publication rates, and factors contributing to publication.

PURPOSE The purposes of this study were to describe the demographics of abstracts presented at the prosthodontics section of IADR General Sessions from 2004 to 2005, evaluate the publication rate of abstracts, and analyze the relationship between variables in abstracts and publication. MATERIALS AND METHODS Prosthodontics research section abstracts from the IADR General Session in 2004 and 2005 were evaluated for: number of authors, presentation type, origin, affiliation, topic, study design, statistics, study outcome, and funding. The publication rate was calculated following a PubMed search. The journal of publication, year of publication, and the length of time before publication were analyzed. Descriptive statistics were used for the data analysis; the relationships between presentation type, study design, study outcome, statistics, funding, and publication were analyzed using logistic regression (α= 0.05). RESULTS From 346 abstracts, 37.0% were published. For oral presentations, 40.7% were published; 35.8% of poster presentations were published. The mean duration before publication was 26.4 months. North America had the most abstracts, and Europe had the most publications. Fixed prosthodontic research had the highest number and proportion for publication. A significant association with publication was noted for neutral study outcomes (p= 0.018), studies with funding (p= 0.035), and abstracts from Europe (p= 0.001). CONCLUSIONS The majority of abstracts from the prosthodontics research section of IADR General Sessions from 2004 and 2005 remain unpublished. A significant association for publication was noted with neutral outcomes, funding, and abstracts from Europe.
The therapeutic challenge of giant splenic artery aneurysm: a case repport

ABSTRACT Giant splenic artery aneurysm is a rare condition that represents an eminent life threatening for the patient, requiring, therefore, urgent surgical correction. A 61-year-old woman, former smoker, hypertensive, hypercholesterolemic and multipara sought our service because of a large tumor in the mesogastrium, which was an abdominal ultrasound finding. Despite the size of the tumor, the patient was asymptomatic. The angiotomography and the magnetic resonance image of the abdomen were suggestive of giant splenic artery aneurysm with more than 10cm in diameter that was confirmed by an angiography. She underwent surgery, open splenectomy, and partial aneurysmectomy. The approach of the celiac artery, which was ligated, was only possible with medialvisceral rotation because there was no possibility to view it through the anterior access. The histopathological test of aneurysmatic wall revealed atheroma plaques in the intima. The patient progressed without complications and she was discharged cured. In general, giant splenic artery aneurysms are symptomatic, however, as in the case we report, it may be asymptomatic and found in abdominal imaging exam. Although less invasive Interventional methods exist, such as laparoscopy and endovascular techniques, they were considered inappropriate in this case. Conventional open surgery should be the therapy of choice for a giant splenic artery aneurysm.