Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Domain Deletion Analysis of the Major Sporulation Kinase in Bacillus subtilis

ABSTRACT To characterize the role of the three PAS domains in KinA, the major sporulation kinase in Bacillus subtilis, we constructed a series of systematic PAS domain deletion mutants and analyzed their activities using an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible artificial sporulation induction system, which we have developed recently. The results showed that any one of the three PAS domains is sufficient to maintain the kinase activity and trigger sporulation, if not fully then at least partially, when the protein levels increase beyond a certain level.
MsFLASH participants’ priorities for alleviating menopausal symptoms

ABSTRACT Objective To describe self-reported menopausal symptom priorities and their association with demographics and other symptoms among participants in an intervention trial for vasomotor symptoms (VMS). Methods Cross-sectional study embedded in the MsFLASH 02 trial, a three-by-two factorial design of yoga vs. exercise vs. usual activity and omega-3-fatty acid vs. placebo. At baseline, women (n = 354) completed hot flush diaries, a card sort task to prioritize symptoms they would most like to alleviate, and standardized questionnaires. Results The most common symptom priorities were: VMS (n = 322), sleep (n = 191), concentration (n = 140), and fatigue (n = 116). In multivariate models, women who chose VMS as their top priority symptom (n = 210) reported significantly greater VMS severity (p = 0.004) and never smoking (p = 0.012), and women who chose sleep as their top priority symptom (n = 100) were more educated (p ≤ 0.001) and had worse sleep quality (p < 0.001). ROC curves identified sleep scale scores that were highly predictive of ranking sleep as a top priority symptom. Conclusions Among women entering an intervention trial for VMS and with relatively low prevalence of depression and anxiety, VMS was the priority symptom for treatment. A card sort may be a valid tool for quickly assessing symptom priorities in clinical practice and research.
Endoscopic Minor Papilla Balloon Dilation for the Treatment of Symptomatic Pancreas Divisum

Objective A subpopulation of patients with pancreas divisum experience symptomatic events such as recurrent acute pancreatitis and chronic pancreatitis. Minor papilla sphincterotomy has been reported as being an effective treatment. The aim of this study was to evaluate the safety and efficacy of endoscopic balloon dilation for the minor papilla. Methods Between 2000 and 2012, 16 patients were retrospectively included in this study. After endoscopic balloon dilation for the minor papilla was received, a pancreatic stent or a nasal pancreatic drainage catheter was placed for 1 week. If a stricture or obstruction was evident, it was treated with balloon dilation followed by long-term stent placement (1 year). When an outflow of pancreatic juice was disturbed by a pancreatic stone, endoscopic stone extraction was performed. Results Balloon dilation and stent placement were achieved and were successful in all the cases (16/16; 100%). Clinical improvement was achieved in 7 (84.7%) of the 9 patients with recurrent acute pancreatitis and in 6 (85.7%) of the 7 patients with chronic pancreatitis. Early complications were observed in 1 (6.3%) patient. Pancreatitis or bleeding related to balloon dilation was not observed. Conclusions Endoscopic balloon dilation for the minor papilla is feasible for the management of symptomatic pancreas divisum.
Ion Transporter NKCC1, Modulator of Neurogenesis in Murine Olfactory Neurons*

Background: NKCC1 is controversially discussed as the main chloride transporter in olfactory epithelium. Results: Lack of NKCC1 results in impaired odorant detection and a decrease in the number of mature neurons. Conclusion: NKCC1 is involved in chloride accumulation but also reveals an impact in neurogenesis. Significance: This work contributes to the understanding of olfactory epithelium neurogenesis. Olfaction is one of the most crucial senses for vertebrates regarding foraging and social behavior. Therefore, it is of particular interest to investigate the sense of smell, its function on a molecular level, the signaling proteins involved in the process and the mechanism of required ion transport. In recent years, the precise role of the ion transporter NKCC1 in olfactory sensory neuron (OSN) chloride accumulation has been a controversial subject. NKCC1 is expressed in OSNs and is involved in chloride accumulation of dissociated neurons, but it had not been shown to play a role in mouse odorant sensation. Here, we present electro-olfactogram recordings (EOG) demonstrating that NKCC1-deficient mice exhibit significant defects in perception of a complex odorant mixture (Henkel100) in both air-phase and submerged approaches. Using next generation sequencing (NGS) and RT-PCR experiments of NKCC1-deficient and wild type mouse transcriptomes, we confirmed the absence of a highly expressed ion transporter that could compensate for NKCC1. Additional histological investigations demonstrated a reduced number of cells in the olfactory epithelium (OE), resulting in a thinner neuronal layer. Therefore, we conclude that NKCC1 is an important transporter involved in chloride ion accumulation in the olfactory epithelium, but it is also involved in OSN neurogenesis.
The Genetic Architecture of Domestication in Animals

Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the “domestication phenotype. ” In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.
Properties and limits of some essential oils: chemical characterisation, antimicrobial activity, interaction with antibiotics and cytotoxicity

Abstract Because of the emergence of multi-drug resistance bacteria and fungi, alternatives to conventional antimicrobial therapy are needed. This study aims to evaluate in vitro the antimicrobial activity of: Mirtus communis, Coriandrum sativum, Pelargonium capitatum, Cuminum cyminum, Ocimum basilicum, Citrus aurantium amara, Cymbopogon. winterianus, Cymbopogon martini, Salvia sclarea, Melaleuca alternifolia and Mentha suaveolens essential oils on bacteria and fungi, in relation to their chemical composition. The potential interaction of M. alternifolia (TTO), C. sativum (CDO) and M. suaveolens (EOMS) essential oils when used in combination with gentamicin and fluconazole has been evaluated. The results obtained showed a synergic effect on some bacteria and fungi, with FICI values ≤5. The cytotoxicity of TTO, CDO and EOMS was investigated towards HeLa cells. Only EOMS did not result cytotoxic at the active concentrations on micro-organisms. Further studies are necessary to obtain optimal ratios and dosing regimens for higher therapeutic efficacy and to decrease toxicological profiles.
A new class of efficient adaptive nonlinear filters (ANLF)

A multilinearization procedure is described, with the use of which a new class of algorithms for nonlinear filtering can be realized. The methodology targets on adaptively selecting the best reference points for linearization from an ensemble of generated trajectories that span the whole state space of the desired signal. Through simulations, the approach is shown to be significantly superior to the classical extended Kalman filter and comparable in computational burden.
Age at onset of anorexia nervosa and breast cancer risk

The objective of this study was to investigate breast cancer occurrence among women treated for anorexia nervosa (AN), with emphasis on age at the onset of this disorder. We conducted a register-based retrospective cohort with a total of 6009 women with at least one admission with an AN diagnosis during the period 1973–2003 in Sweden. During a mean follow-up of 13.4 years, information on 80 057 women-years was generated. The standardized incidence ratio (SIR) – the ratio of observed-to-expected number of cases – was used as the measure of relative risk. Overall, 16 women developed breast cancer versus 25.5 expected cases [SIR: 0.6, 95% confidence interval (CI): 0.4–0.9]. Among women who were first admitted for AN between the age of 10 and 24 years, four developed breast cancer versus 11.3 expected (SIR: 0.4, 95% CI: 0.1–0.9). In this group of women with early onset AN, only one parous woman developed breast cancer versus 6.3 expected (SIR: 0.2, 95% CI: 0–0.9). Among women first hospitalized for AN between the age of 25 and 40 years, 12 developed breast cancer, whereas the expected number was 14.2, a nonsignificant deficit. Our results suggest that early onset AN may play an important role in the development of breast cancer, possibly because of the extreme restriction of energy intake at a crucial period for mammary gland development. Late onset AN is likely to play a relatively less important role.
Anatomical considerations for endoscopic endonasal skull base surgery in pediatric patients

Pediatric skull base surgery is limited by several boney sinonasal landmarks that must be overcome prior to tumor dissection. When approaching a sellar or parasellar tumor, the piriform aperture, sphenoid sinus pneumatization, and intercarotid distances are areas of potential limitation. Quantitative pediatric anatomical measurements relevant to skull base approaches are lacking. Our goal was to use radio‐anatomic analysis of computed tomography scans to determine anatomical limitations for trans‐sphenoidal approaches in pediatric skull base surgery.
Variation in Dialysis Quality Measures by Facility, Neighborhood, and Region

Background:We examined whether dialysis facility characteristics, neighborhood demographics, and region are associated with Centers for Medicare and Medicaid Services (CMS) dialysis facility quality measures in order to determine the most important targets for intervention. Methods:We linked US census data to the CMS Dialysis Compare File which contains information for facility outcomes for all CMS-certified dialysis facilities in 2007 (n=5616). We then used linear and logistic regression to characterize the association between dialysis facility quality—worse than expected patient survival, and the proportion of individuals in a facility achieving dialysis adequacy (urea reduction rate >65) or target hemoglobin (10<Hgb<12 g/dL)—and dialysis facility characteristics, neighborhood demographics, and region. Results:Only an increasing proportion of African Americans in the neighborhood is consistently associated with worse dialysis facility outcomes, even after controlling for neighborhood poverty. Facilities with the highest proportion of African Americans in the neighborhood had worse patient survival [odds ratio (OR) 4.6; 95% confidence interval (CI), 2.8–7.6], were less likely to have adequate dialysis (&bgr; −1.4; 95% CI, −2.3 to −0.6), and achieve targeted hemoglobin (&bgr; −3.1; 95% CI, −4.7 to −1.6) compared to those with the lowest proportion. No other predictor—facility, neighborhood, or region—was consistently associated with dialysis facility quality. Conclusions:The proportion of African Americans in the dialysis facility neighborhood is strongly and consistently associated with lower facility quality. Quality improvement efforts are particularly needed for dialysis facilities in minority communities.
Mutation and Clinical Characteristics of Autosomal-Dominant Hereditary Spastic Paraplegias in China

Background: Hereditary spastic paraplegias constitute a heterogeneous group of inherited neurodegenerative disorders. To date, there has been no systematic mutation and clinical analysis for a large group of autosomal-dominant hereditary spastic paraplegias in China. Objective: The purpose of this study was to investigate the mutation frequencies and the clinical phenotypes of Chinese spastic paraplegia patients. Methods: Direct sequencing and a multiplex ligation-dependent probe amplification assay were applied to detect the mutations of SPAST and ATL1 in 54 autosomal-dominant hereditary spastic paraplegia probands and 66 isolated cases. Next, mutations in NIPA1, KIF5A, REEP1 and SLC33A1 were detected in the negative patients. Subsets of spastic paraplegia patients were genotyped for the modifying variants. Further, detailed clinical data regarding the genetically diagnosed families were analysed. Results: Altogether, 27 families were diagnosed as SPG4, 3 as SPG3A and 1 as SPG6. No mutations in KIF5A, REEP1 or SLC33A1 were found; 9 SPAST mutations were novel. There was no p.S44L or p.P45Q variant in SPAST and no p.G563A variant in HSPD1 in either the 120 spastic paraplegia patients or the 500 controls. There was a remarkable clinical difference between the SPG4 and non-SPG4 patients and even between genders among the SPG4 patients. Non-penetrance and remarkable gender difference were observed in some SPG4 and SPG3A families. Conclusions: Our data confirm that hereditary spastic paraplegias in China represent a heterogeneous group of genetic neurodegenerative disorders in autosomal-dominant and apparently sporadic forms. Novel genotype-phenotype correlations were established.
Forecast of Dengue Incidence Using Temperature and Rainfall

Introduction An accurate early warning system to predict impending epidemics enhances the effectiveness of preventive measures against dengue fever. The aim of this study was to develop and validate a forecasting model that could predict dengue cases and provide timely early warning in Singapore. Methodology and Principal Findings We developed a time series Poisson multivariate regression model using weekly mean temperature and cumulative rainfall over the period 2000–2010. Weather data were modeled using piecewise linear spline functions. We analyzed various lag times between dengue and weather variables to identify the optimal dengue forecasting period. Autoregression, seasonality and trend were considered in the model. We validated the model by forecasting dengue cases for week 1 of 2011 up to week 16 of 2012 using weather data alone. Model selection and validation were based on Akaike's Information Criterion, standardized Root Mean Square Error, and residuals diagnoses. A Receiver Operating Characteristics curve was used to analyze the sensitivity of the forecast of epidemics. The optimal period for dengue forecast was 16 weeks. Our model forecasted correctly with errors of 0.3 and 0.32 of the standard deviation of reported cases during the model training and validation periods, respectively. It was sensitive enough to distinguish between outbreak and non-outbreak to a 96% (CI = 93–98%) in 2004–2010 and 98% (CI = 95%–100%) in 2011. The model predicted the outbreak in 2011 accurately with less than 3% possibility of false alarm. Significance We have developed a weather-based dengue forecasting model that allows warning 16 weeks in advance of dengue epidemics with high sensitivity and specificity. We demonstrate that models using temperature and rainfall could be simple, precise, and low cost tools for dengue forecasting which could be used to enhance decision making on the timing, scale of vector control operations, and utilization of limited resources.
Vps4A functions as a tumor suppressor by regulating the secretion and uptake of exosomal microRNAs in human hepatoma cells

The deregulation of microRNAs (miRNAs) plays an important role in human hepatocarcinogenesis. In this study, we highlight exosomes as mediators involved in modulating miRNA profiles in hepatocellular carcinoma (HCC) cells. First, we examined the different miRNA expression profiles in HCC cells and HCC cell–derived exosomes. Next, coculture experiments indicated that HCC cell–derived exosomes promoted the cell growth, migration, and invasion of HCC cells and had the ability to shuttle miRNAs to recipient cells. Further, our data showed that Vps4A, a key regulator of exosome biogenesis, was frequently down‐regulated in HCC tissues. The reduction of Vps4A in HCC tissues was associated with tumor progression and metastasis. In vitro studies revealed that Vps4A repressed the growth, colony formation, migration, and invasion of HCC cells. We further investigated the role and involvement of Vps4A in suppressing the bioactivity of exosomes and characterized its ability to weaken the cell response to exosomes. By small RNA sequencing, we demonstrated that Vps4A facilitated the secretion of oncogenic miRNAs in exosomes as well as accumulation and uptake of tumor suppressor miRNAs in cells. A subset of Vps4A‐associated miRNAs was identified. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that the phosphatidylinositol‐3‐kinase/Akt signaling pathway was the most likely candidate pathway for modulation by these miRNAs. Indeed, we proved that the phosphatidylinositol‐3‐kinase/Akt pathway was inactivated by Vps4A overexpression. Conclusion: Exosome‐mediated miRNA transfer is an important mechanism of self‐modulation of the miRNA expression profiles in HCC cells, and Vps4A may function as a tumor suppressor, which utilizes exosomes as mediators to regulate the secretion and uptake of miRNAs in hepatoma cells; these observations provide new insights into the development of HCC. (Hepatology 2015;61:1284–1294)
Quercetin impairs the reproductive potential of male mice

Oxidative stress is a leading cause of male infertility. To combat this, germ cells and spermatozoa are endowed with various enzymes, vitamins and proteins. Certain other components of food, including bioflavonoids, also provide protection against free radicals. This study analysed the effect of quercetin, a bioflavonoid, on male reproductive function in adult mice, after intraperitoneal treatment with varying concentrations of quercetin (2, 8 and 20 mg kg−1 b.wt.) for 2 weeks. Quercetin increased the generation of reactive oxygen species and lipid peroxidation in the testis with concomitant decrease in sperm count and motility in a dose‐dependent manner. Activities of antioxidant enzymes catalase, superoxide dismutase and levels of reduced glutathione were found to be decreased in a dose‐dependent manner. Also, the levels of oxidised glutathione were increased leading to a shift in redox ratio. The testicular histomorphology was also altered dose dependently. Germ cell kinetic study revealed significant loss of various germ cell populations with increasing dose of quercetin. Interestingly, there was a reduction in germinal epithelium thickness concomitant with an increase in seminiferous tubule lumen diameter. In conclusion, the deleterious effects of quercetin on germ cells could be attributed to its pro‐oxidant ability that might affect the Sertoli cell functions.
Long-Term In vivo Effects of Cisplatin on γ-H2AX Foci Signaling in Peripheral Lymphocytes of Tumor Patients After Irradiation

Purpose: This study determined the effects of cis-diamminedichloroplatinum(II) on radiation-induced foci formation of γ-H2AX and Rad51 in lymphocytes. Experimental Design: Twenty-eight cancer patients were irradiated for intrathoracic, pelvic, or head and neck tumors and received simultaneous cisplatin containing chemotherapy. The effect of cisplatin on radiation-induced γ-H2AX and Rad51 foci as a response to ionizing radiation–induced DNA double-strand breaks was measured in lymphocytes after in vivo and in vitro radiochemotherapy. The role of DNA-dependent protein kinase and ataxia-telangiectasia mutated kinase in γ-H2AX signaling, the consequences of altered γ-H2AX foci formation on double-strand break end joining, was studied. Results: Cisplatin decreased the number of induced γ-H2AX foci in lymphocytes after in vivo or in vitro irradiation by 34% ± 6% at days 0 to 3 after cisplatin (P < 0.0001) and remained significant until day 6. The variation in this cisplatin effect from patient to patient was larger than the retest error within the same patient (P = 0.01). The cisplatin effect was not accompanied by an inhibition of end joining of double-strand break as analyzed using gel electrophoresis of DNA under neutral conditions. Cisplatin also decreased radiation induced Rad51 foci formation in lymphocytes after stimulation of proliferation with phytohemagglutinin by 47% ± 6% (P < 0.0001). Conclusion: Cisplatin has long-term effects on the early double-strand break response of γ-H2AX and Rad51 foci formation after ionizing radiation. Inhibition of sensing and processing of double-strand break by γ-H2AX and Rad51 foci formation are important mechanisms by which cisplatin can alter the radiation response.
Adding tails to $C^*$-correspondences

We describe a method of adding tails to C*-correspondences which generalizes the process used in the study of graph C*-algebras. We show how this technique can be used to extend results for augmented Cuntz-Pimsner algebras to C*-algebras associated to general C*-correspondences, and as an application we prove a gauge-invariant uniqueness theorem for these algebras. We also define a notion of relative graph C*-algebras and show that properties of these C*-algebras can provide insight and motivation for results about relative Cuntz-Pimsner algebras.
Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ∼40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.
A GRASP based heuristic for Deployment Roadside Units in VANETs

In this work we propose a new algorithm, Delta-r-GRASP, for solving the allocation of Roadside Units (RSUs) in a Vehicular Network. Our goal is to find the minimum set of RSUs to meet a Deployment Δ<inf>ρ2</inf><sup>ρ1</sup>. The Deployment Δ<inf>ρ2</inf><sup>ρ1</sup> is a metric for specifying minimum communication guarantees from the infrastructure supporting the Vehicular Network. We compare our algorithm with a baseline algorithm, Delta-r. Moreover, we compare our results with the optimal value achieved by solver CPLEX. Our results demonstrate that our approach requires up to 85% fewer RSUs to achieve the same deployment efficiency, and our results differ no more than 15% from the optimal values.