Miracle-dz/UniFAR-FTUs huggingface dataset:
Beneficial effects of treadmill training in experimental diabetic nerve regeneration

OBJECTIVES: We investigated the effects of treadmill training (10 weeks) on hindlimb motor function and nerve morphometric parameters in diabetic rats submitted to sciatic nerve crush. MATERIALS AND METHOD: Wistar rats (n = 64) were divided into the following groups: non-diabetic; trained non-diabetic; non-diabetic with sciatic nerve crush; trained non-diabetic with sciatic nerve crush; diabetic; trained diabetic; diabetic with sciatic nerve crush or trained diabetic with sciatic nerve crush. Diabetes was induced by streptozotocin injection (50 mg/kg, iv). Hindlimb motor function was evaluated weekly by assessing sciatic functional indices, and the proximal and distal portions of the sciatic nerve were used for morphometric analysis. RESULTS: At 13 weeks post-injury, the distal nerve portion of all injured groups and the proximal nerve portion of the diabetic with sciatic nerve crush group presented altered morphometric parameters such as decreased myelinated fiber diameter (∼7.4±0.3µm vs ∼4.8±0.2µm), axonal diameter (∼5±0.2µm vs ∼3.5±0.1µm) and myelin sheath thickness (∼1.2±0.07µm vs ∼0.65±0.07µm) and an increase in the percentage of area occupied by endoneurium (∼28±3% vs ∼60±3%). In addition, in the non-diabetic with sciatic nerve crush group the proximal nerve portion showed a decreased myelinated fiber diameter (7.4±0.3µm vs 5.8±0.3µm) and myelin sheath thickness (1.29±0.08µm vs 0.92±0.08µm). The non-diabetic with sciatic nerve crush, trained non-diabetic with sciatic nerve crush, diabetic with sciatic nerve crush and trained diabetic with sciatic nerve crush groups showed normal sciatic functional index from the 4th, 4th, 9th and 7th week post-injury, respectively. Morphometric alterations in the proximal nerve portion of the diabetic with sciatic nerve crush and non-diabetic with sciatic nerve crush groups were either prevented or reverted to values similar to the non-diabetic group by treadmill training. CONCLUSION: Diabetic condition promoted delay in sciatic nerve regeneration. Treadmill training is able to accelerate hindlimb motor function recovery in diabetic injured rats and prevent or revert morphometric alterations in proximal nerve portions in non-diabetic and diabetic injured rats.
Plasmonic octagonal quasicrystals for surface enhanced Raman sensing

Abstract Surface enhanced Raman scattering (SERS) on eight-fold quasicrystal arrays with precisely controlled size and spacing fabricated via electron beam lithography was investigated. This SERS substrate shows high efficiency at 785 nm excitation in the detection of p-mercaptoaniline (pMA), and a SERS enhancement factor (EF ) of 107 is achieved. SERS behavior of the realized engineered SERS substrate indicates that the present engineered metamaterial may be used as an ultrasensitive Raman probe and could open up interesting new opportunities in biosensing.
Paraneoplastic Cushing's syndrome associated to locally advanced thymic carcinoid tumor.

BACKGROUND Thymic carcinoid is a frequent cause of Cushing's syndrome due to ectopic adrenocorticotropin secretion. Histology and immunohistochemistry allow differential diagnosis from other epithelial thymic tumors, such as thymomas and thymic carcinomas. The term used to name this tumor is confusing, since it is a malignant neuroendocrine neoplasm, and therapeutic approaches need to bear that in mind. CASE REPORT Unlike most cases of thymic carcinoid associated to Cushing's syndrome that had distant metastases at diagnosis, we report a 50-year-old male who presented with Cushing's syndrome and was diagnosed with thymic carcinoid without distant metastases. Multimodal treatment with surgery, radiotherapy and chemotherapy (cisplatin plus etoposide) induced a complete clinical and biochemical remission lasting for 46 months.
Azathioprine versus mesalazine for prevention of postoperative clinical recurrence in patients with Crohn's disease with endoscopic recurrence: efficacy and safety results of a randomised, double-blind, double-dummy, multicentre trial

Objective The aim of the study was to compare azathioprine versus mesalazine tablets for the prevention of clinical recurrence in patients with postoperative Crohn's disease (CD) with moderate or severe endoscopic recurrence. Methods This was a 1 year, double-blind, double-dummy, randomised study which took place in 21 gastroenterology centres in Austria, the Czech Republic, Germany and Israel. The study participants were 78 adults with CD who had undergone resection with ileocolonic anastomosis in the preceding 6–24 months without subsequent clinical recurrence and with a Crohn's disease activity index (CDAI) score <200, but with moderate or severe endoscopic recurrence. The study drugs were azathioprine 2.0–2.5 mg/kg/day or mesalazine 4 g/day over 1 year. The primary end point was therapeutic failure during 1 year, defined as a CDAI score ≥200 and an increase of ≥60 points from baseline, or study drug discontinuation due to lack of efficacy or intolerable adverse drug reaction. Results Treatment failure occurred in 22.0% (9/41) of azathioprine-treated patients and 10.8% (4/37) of mesalazine-treated patients, a difference of 11.1% (95% CI −5.0% to 27.3%, p=0.19). Clinical recurrence was significantly less frequent with azathioprine versus mesalazine (0/41 (0%) vs 4/37 (10.8%), p=0.031), whereas study drug discontinuation due to adverse drug reactions only occurred in azathioprine-treated patients (9/41 (22.0%) vs 0%, p=0.002). The proportion of patients showing ≥1 point reduction in Rutgeerts score between baseline and month 12 was 63.3% (19/30) and 34.4% (11/32) in the azathioprine and mesalazine groups, respectively (p=0.023). Conclusions In this population of patients with postoperative CD at high risk of clinical recurrence, superiority for azathioprine versus mesalazine could not be demonstrated for therapeutic failure. Clinical trial registration number NCT00946946.
Association between genetic polymorphisms of the IL28B gene and leukomonocyte in Chinese hepatitis B virus-infected individuals

Background Hepatitis B infection is one of the most severe hepatic diseases in China. Thus, understanding the genetic pathogenesis of hepatitis B virus (HBV)-infected individuals is important. Although no consistent result is obtained in different populations, HBV treatment effect is reportedly associated with the IL28B gene. Methods To investigate the role of the IL28B gene in HBV-infected individuals in Yunnan, China, we screened genotypes of three single nucleotide polymorphisms (SNPs, rs12979860, rs8099917, and rs12980275) in HBV-infected individuals and general controls by using SnapShot and sequencing. Results Results showed no significant difference was found in genotypes, alleles, and haplotypes frequency between the HBV-infected individuals and controls. After dividing the HBV-infected individuals into patients in acute infection, chronic HBV patients, and patients undergoing convalescence, the genotype GT (P = 0.033) and allele G (P = 0.038) of rs8099917 showed statistically higher frequency in the acutely infectious individuals than in the HBV patients undergoing convalescence. HBV viral load was higher in the acutely infectious patients than in the chronic infection group. Strikingly, we found that leukomonocyte (LYM) level was associated with SNPs in the IL28B gene. In addition, the LYM levels were lower in the HBV-infected individuals with genotype CC of rs12979860 and AA of rs12980275 than in the patients with other genotypes of these two SNPs. Conclusion Our results suggested genetic polymorphisms of the IL28B gene were associated with LYM level of HBV-infected individuals.
NGAL Expression Is Elevated in Both Colorectal Adenoma–Carcinoma Sequence and Cancer Progression and Enhances Tumorigenesis in Xenograft Mouse Models

Purpose: There is growing evidence implicating that neutrophil gelatinase–associated lipocalin (NGAL) plays a role in the development and progression of cancers. However, the effect of NGAL in colorectal carcinoma (CRC) has not been clearly elucidated. In this study, we investigated the role of NGAL in the tumorigenesis and progression of CRC and evaluated the clinical value of NGAL expression. Experimental Design: We examined NGAL expression in 526 colorectal tissue samples, including 53 sets of matched specimens (histologically normal mucosa, adenomas, and carcinomas) using immunohistochemical analysis. In CRCs, correlations between NGAL expression and clinicopathologic parameters were analyzed, and survival analysis was conducted. The role of NGAL was further tested using mouse xenograft models. Results: NGAL expression was elevated during the colorectal adenoma–carcinoma sequence both among the 526 cases (rs = 0.66, P < 0.001) and in the 53 sets of matched specimens (rs = 0.60, P < 0.001). In CRCs, NGAL expression was associated with cancer stage (P = 0.041) and tumor recurrence in stage II patients (P = 0.037). Survival analysis revealed that NGAL expression was an independent prognostic factor for overall survival (HR = 1.84, P = 0.004) and for disease-free survival of stage II patients (HR = 5.88, P = 0.021). In mouse models, the xenografts in cecum and spleen were heavier and more numerous in the group injected with NGAL-overexpressing CRC cells (P < 0.05). Conclusions: NGAL overexpression may promote the tumorigenesis and progression of CRC. Detecting NGAL expression in tumor tissues may be useful for evaluating prognosis of patients with CRC. Clin Cancer Res; 17(13); 4331–40. ©2011 AACR.
Heat transfer analysis of the plasma-spray deposition process

A novel approach has been used to analyse the flow of heat during the plasma spray coating process. The approach couples heat transfer processes occurring at the micro scale, within the coating, and at the macro scale, in the substrate, using a combination of finite-element and finite-difference based models. One of the key boundary conditions employed in the model has been determined from an inverse heat conduction analysis of data recorded from an array of thermocouples embedded into a copper disk while being sprayed with a stationary gun in the absence of powder deposition. The models have been used to determine the evolution of temperature in 8 wt% yttria partially stabilized zirconia coatings deposited onto AISI-1008 steel for the deposition times of 1, 2 and 3 seconds. The results indicate that the cooling rate of the 7 material deposited initially is of the order of 10 °C/s and that the first splat cools from its -3 melting temperature to room temperature in approximately 10 s. The predictions from the model have been compared qualitatively with the distribution and the shape of pores found in the coating after subsequent metallographic examination. Different size and distribution of pores found at different locations of the zirconia based coating appear consistent with a qualitative understanding of the evolution of temperature in the coatings examined. Pores located at the coating / substrate interface appeared larger and were inter-connected. At the centre near the free surface of the coating, however, pores were closed and isolated. In addition, the same models have been applied for the plasma spray deposition of 17% Co-WC and CP titanium on AISI-1008 steel. The particle temperatures predicted using the model were compared with the temperatures measured in an independent study using a pyrometer-based measurements on the same plasma spray system. The results of the heat flow-based analysis were found to agree with the pyrometer-based measurements to within 10% for the case of 17% Co-WC and to within 16% for CP titanium.
Precipitation hardening of HSLA steels

A process model to describe the strength contributior from precipitation hardening during coiling after hot rolling has been developed for V and Nb HSLA steels. Experimental measurements of ageing behaviour on the V steel were conducted on coil material which was received in an underaged condition. The size and composition of precipitates was examined on replicas using scanning transmission electron microscopy. The precipitates were observed to be V rich and a substantial increase in precipitate size occurred as a function of ageing time. The modelling approach developed by Shercliff and Ashby for aluminium alloys was extended to microalloyed steels. The model assumes particle coarsening is the rate controlling process and that the precipitates are initially sheared by dislocations with a transition to non-shearable precipitates at peak strength. After calibration of the model, good agreement was observed between the model predictions and-experimental data. A model for ageing in a Nb HSLA steel was also developed using literature values for the ageing behaviour.
Next-Generation Sequencing Identifies MicroRNAs that Associate with Pathogenic Autoimmune Neuroinflammation in Rats

MicroRNAs (miRNAs) are known to regulate most biological processes and have been found dysregulated in a variety of diseases, including multiple sclerosis (MS). In this study, we characterized miRNAs that associate with susceptibility to develop experimental autoimmune encephalomyelitis (EAE) in rats, a well-established animal model of MS. Using Illumina next-generation sequencing, we detected 544 miRNAs in the lymph nodes of EAE-susceptible Dark Agouti and EAE-resistant Piebald Virol Glaxo rats during immune activation. Forty-three miRNAs were found differentially expressed between the two strains, with 81% (35 out of 43) showing higher expression in the susceptible strain. Only 33% of tested miRNAs displayed differential expression in naive lymph nodes, suggesting that a majority of regulated miRNAs are EAE dependent. Further investigation of a selected six miRNAs indicates differences in cellular source and kinetics of expression. Several of the miRNAs, including miR-146a, miR-21, miR-181a, miR-223, and let-7, have previously been implicated in immune system regulation. Moreover, 77% (33 out of 43) of the miRNAs were associated with MS and other autoimmune diseases. Target genes likely regulated by the miRNAs were identified using computational predictions combined with whole-genome expression data. Differentially expressed miRNAs and their targets involve functions important for MS and EAE, such as immune cell migration through targeting genes like Cxcr3 and cellular maintenance and signaling by regulation of Prkcd and Stat1. In addition, we demonstrated that these three genes are direct targets of miR-181a. Our study highlights the impact of multiple miRNAs, displaying diverse kinetics and cellular sources, on development of pathogenic autoimmune inflammation.
California’s Cap-and-Trade Market Through 2030: A Preliminary Supply/Demand Analysis

∗ This research was supported by a grant from the Energy Foundation. The authors were members of the Emissions Market Assessment Committee and Market Simulation Group that advised the California Air Resources Board (ARB) in 2012-2014. The opinions in this paper do not necessarily represent those of the ARB or any of its employees. Email addresses: Borenstein: severinborenstein@berkeley.edu; Bushnell: jbbushnell@ucdavis.edu; Wolak: wolak@stanford.edu.
Occupational injuries among older workers with disabilities: a prospective cohort study of the Health and Retirement Survey, 1992 to 1994.

OBJECTIVES We tested the hypothesis that among older workers, disabilities in general, and hearing and visual impairments in particular, are risk factors for occupational injuries. METHODS Using the first 2 interviews of the Health and Retirement Study, a nationally representative survey of Americans aged 51 to 61 years, we conducted a prospective cohort study of 5600 employed nonfarmers. RESULTS Testing a logistic regression model developed in a previous cross-sectional study, we found that the following occupations and risk factors were associated with occupational injury as estimated by odds ratios: service personnel, odds ratio = 1.71 (95% confidence interval = 1.13, 2.57); mechanics and repairers, 3.47 (1.98, 6.10); operators and assemblers, 2.33 (1.51, 3.61); laborers, 3.16 (1.67, 5.98); jobs requiring heavy lifting, 2.05 (1.55, 2.70); self-employment, 0.50 (0.34, 0.73); and self-reported disability, 1.58 (1.14, 2.19). Replacing the general disability variable with specific hearing and visual impairment variables, we found that poor hearing (1.35 [0.95, 1.93]) and poor sight (1.45 [0.94, 2.22]) both had elevated odds ratios. CONCLUSIONS Poor sight and poor hearing, as well as work disabilities in general, are associated with occupational injuries among older workers.
Effective Ways of Secure, Private and Trusted Cloud Computing

Cloud computing is an Internet-based computing, where shared resources, software and information, are provided to computers and devices on-demand. It provides people the way to share distributed resources and services that belong to different organization. Since cloud computing uses distributed resources in open environment, thus it is important to provide the security and trust to share the data for developing cloud computing applications. In this paper we assess how can cloud providers earn their customers’ trust and provide the security, privacy and reliability, when a third party is processing sensitive data in a remote machine located in various countries? A concept of utility cloud has been represented to provide the various services to the users. Emerging technologies can help address the challenges of Security, Privacy and Trust in cloud computing.
The use of description logics in KBSE systems

The increasing size and complexity of many software systems demand a greater emphasis on capturing and maintaining knowledge at many different levels within the software development process. The knowledge-based software engineering (KBSE) research paradigm is concerned with systems that use formally represented knowledge, with associated inference procedures, to support the various subactivities of software development. As they grow in scale, KBSE systems must balance expressivity and inferential power with the real demands of knowledge base construction, maintenance, performance and comprehensibility. Description logics (DL's) possess several features - a terminological orientation, a formal semantics and efficient reasoning procedures - which offer an effective tradeoff of these factors. We discuss three KBSE systems in which DL's capture some of the requisite knowledge needed to support design, coding and testing activities. We close with a discussion of the benefits of DL's and ways to address some of their limitations. <<ETX>>
The 7 Th Ieee International Conference on Intelligent Data Acquisition and Advanced Computing Systems: Technology and Applications Using Prior Measurements to Improve Probabilistic-based Indoor Localization Methods

– In this paper, we enhance a probabilistic method for determining the position of an unknown node in an indoor environment. Previous work shows that using a small subset of sensors with a probabilistic localization technique reduces the error in comparison to a large set of sensors. Because probability based models rely on a prior distribution for the unknown node, we propose that reference measurements performed at the time of deployment are used to improve the distribution model. We show this new method reduces the estimated location error and increases the likelihood of selecting the correct room.
Fighting Zombies in Minecraft With Deep Reinforcement Learning

In this project, we train an agent in the video game Minecraft to kill as many zombies and survive as long as possible using reinforcement learning. Our agent is only equipped with a sword to attack the zombies while the zombies attack back and try to kill the agent. Our objective is to have the agent learn what policies to execute based solely on the pixels of the gameplay screen. Rather than giving the agent information about the environment or any guidance on killing zombies, it has to learn optimal actions based on its past experience.
The influence of the maternal thyroid hormone environment during pregnancy on the ontogenesis of brain and placental ornithine decarboxylase activity in the rat.

The influence of maternal hypothyroxinaemia on early brain and placental development was examined in a partially thyroidectomized (parathyroid-spared; TX) rat dam model. Ornithine decarboxylase (ODC) specific activity, along with more general indices of cell growth, were determined in prenatal whole brain (at 15, 19 and 22 days of gestation), postnatal brain regions (at 5, 10 and 14 days) and placenta. Maternal hypothyroxinaemia resulted in reductions in fetal body weight, brain weight, brain DNA content and brain total protein content at 15 days of gestation; the latter effect persisting until 19 days of gestation. Further changes in brain cell growth were observed near term, when an increase in the DNA concentration was accompanied by a decrease in the total protein:DNA ratio. Growth of the postnatal brain regions appeared normal, with the exception of an isolated increase in the protein content of the cerebellum at postnatal day 5. Determination of the specific activity of brain ODC revealed a complex pattern of change in the progeny of TX dams, superimposed upon the normal ontogenetic decline. In the fetal brain, activity was initially deficient at 15 days of gestation but was increased at 22 days of gestation relative to controls. The compromise extended into the postnatal period; ODC specific activity being transiently reduced in the brainstem, the subcortex and the cerebral cortex. Placental development was less consistently affected; wet weight, gross indices of cell growth (DNA content, DNA concentration, total protein:DNA ratio) and ODC specific activity were all normal in the TX dam. However, cytosolic and total protein concentrations were reduced at 15 and 19 days of gestation respectively. (ABSTRACT TRUNCATED AT 250 WORDS)
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine

Motivation Despite significant efforts in expert curation, clinical relevance about most of the 154 million dbSNP reference variants (RS) remains unknown. However, a wealth of knowledge about the variant biological function/disease impact is buried in unstructured literature data. Previous studies have attempted to harvest and unlock such information with text-mining techniques but are of limited use because their mutation extraction results are not standardized or integrated with curated data. Results We propose an automatic method to extract and normalize variant mentions to unique identifiers (dbSNP RSIDs). Our method, in benchmarking results, demonstrates a high F-measure of ∼90% and compared favorably to the state of the art. Next, we applied our approach to the entire PubMed and validated the results by verifying that each extracted variant-gene pair matched the dbSNP annotation based on mapped genomic position, and by analyzing variants curated in ClinVar. We then determined which text-mined variants and genes constituted novel discoveries. Our analysis reveals 41 889 RS numbers (associated with 9151 genes) not found in ClinVar. Moreover, we obtained a rich set worth further review: 12 462 rare variants (MAF ≤ 0.01) in 3849 genes which are presumed to be deleterious and not frequently found in the general population. To our knowledge, this is the first large-scale study to analyze and integrate text-mined variant data with curated knowledge in existing databases. Our results suggest that databases can be significantly enriched by text mining and that the combined information can greatly assist human efforts in evaluating/prioritizing variants in genomic research. Availability and implementation The tmVar 2.0 source code and corpus are freely available at https://www.ncbi. nlm.nih.gov/research/bionlp/Tools/tmvar/. Contact zhiyong.lu@nih.gov.