Miracle-dz/UniFAR-FTUs huggingface dataset:
Human diabetic endoneurial sorbitol, fructose, and myo‐inositol related to sural nerve morphometry

Fascicles of the sural nerve from each of 20 diabetic patients, mostly with maturity‐onset diabetes, were studied by biochemical and pathological techniques, and results were compared to values found in nerve specimens from 15 healthy persons. The sorbitol and fructose content was much more variable in diabetic than in healthy nerves. More than one‐third of the diabetic nerves had sorbitol and fructose values above the highest levels for controls. myo‐Inositol and scyllo‐inositol content was not reduced in diabetic nerves. The sorbitol, fructose, and inositol concentrations could not be related to clinical, neurophysiological, or pathological severity of neuropathy. A comparison of scored symptoms and signs and clinical neurophysiological studies against morphometric and teased fiber studies of sural nerve demonstrated that the former three provide sensitive and reliable measures of severity of neuropathy that can be used for controlled clinical trials of diabetic neuropathy. The presence and type of teased fiber abnormalities could be related to the duration of diabetes and to symptoms of neuropathy. In untreated diabetics without symptoms of neuropathy, a higher than normal frequency of teased fibers showing segmental demyelination and remyelination was found. Untreated diabetics with symptomatic neuropathy showed two kinds of abnormalities: fibers with segmental demyelination and remyelination and fibers undergoing axonal degeneration. In treated diabetics, who often had longstanding neuropathy, the most common abnormalities were fibers undergoing axonal degeneration.
An application of linear SVM to fingerprint image segmentation

An exact fingerprint image segmentation improves the accuracy of automatic fingerprint identification system and reduces the processing time of follow-up process. A novel fingerprint image segmentation method based on linear Support Vector Machine (SVM) is proposed to overcome the shortcomings of present approaches shown in previous literatures. Feature vectors are constructed by Fourier spectrum energy ratio and gray contrast extracted from sub-blocks of the fingerprint image. Then these feature vectors are classified by linear SVM, morphological operations are performed to realize fingerprint image segmentation in the end. Experimental results show that this method is precise and reliable compared with other approaches.
Mechanism of inhibition of Ψ+ prion determinant propagation by a mutation of the N‐terminus of the yeast Sup35 protein

The SUP35 gene of Saccharomyces cerevisiae encodes the polypeptide chain release factor eRF3. This protein (also called Sup35p) is thought to be able to undergo a heritable conformational switch, similarly to mammalian prions, giving rise to the cytoplasmically inherited Ψ+ determinant. A dominant mutation (PNM2 allele) in the SUP35 gene causing a Gly58→Asp change in the Sup35p N‐terminal domain eliminates Ψ+. Here we observed that the mutant Sup35p can be converted to the prion‐like form in vitro, but such conversion proceeds slower than that of wild‐type Sup35p. The overexpression of mutant Sup35p induced the de novo appearance of Ψ+ cells containing the prion‐like form of mutant Sup35p, which was able to transmit its properties to wild‐type Sup35p both in vitro and in vivo. Our data indicate that this Ψ+‐eliminating mutation does not alter the initial binding of Sup35p molecules to the Sup35p Ψ+‐specific aggregates, but rather inhibits its subsequent prion‐like rearrangement and/or binding of the next Sup35p molecule to the growing prion‐like Sup35p aggregate.
Changes in Molecular Epidemiology of Streptococcus pneumoniae Causing Meningitis following Introduction of Pneumococcal Conjugate Vaccination in England and Wales

ABSTRACT The introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in September 2006 has markedly reduced the burden of invasive pneumococcal disease (IPD) including meningitis in England and Wales. This study examined changes in the molecular epidemiology of pneumococcal isolates causing meningitis from July 2004 to June 2009. The Health Protection Agency conducts enhanced pneumococcal surveillance in England and Wales. In addition to serotyping, pneumococcal isolates causing meningitis were genotyped by multilocus sequence typing (MLST). A total of 1,030 isolates were both serotyped and genotyped over the 5-year period. Fifty-two serotypes, 238 sequence types (STs), and 87 clonal complexes were identified, with no significant difference in the yearly Simpson's diversity index values (range, 0.974 to 0.984). STs commonly associated with PCV7 serotypes declined following PCV implementation, with a proportionally greater decline in ST124 (commonly associated with serotype 14). No other ST showed significant changes in distribution, even within individual serotypes. Replacement disease following PCV7 introduction was mainly due to serotypes 1, 3, 7F, 19A, 22F, and 33F through clonal expansion. A single instance of possible capsule switching was identified where one ST4327 clone expressed a serotype 14 capsule in 2005 and a serotype 28A capsule in 2009. In 2008 to 2009, ST191 (7F) became the most prevalent clone causing meningitis (10.3%). Case fatality (145 fatalities/1,030 cases; 14.1%) was high across all age groups and serotype groups. Thus, the introduction of PCV7 resulted in an increase in non-PCV7 serotypes, including some not covered by the 13-valent vaccine, such as serotypes 22F and 33F, emphasizing the importance of long-term epidemiological and molecular surveillance.
LZAP is a novel Wip1 binding partner and positive regulator of its phosphatase activity in vitro

ABSTRACT The phosphatase Wip1 attenuates the DNA damage response (DDR) by removing phosphorylation marks from a number of DDR proteins (p53, MDM2, Chk1/2, p38). Wip1 also dephosphorylates and inactivates RelA. Notably, LZAP, a putative tumor suppressor, has been linked to dephosphorylation of several of these substrates, including RelA, p38, Chk1, and Chk2. LZAP has no known catalytic activity or functional motifs, suggesting that it exerts its effects through interaction with other proteins. Here we show that LZAP binds Wip1 and stimulates its phosphatase activity. LZAP had been previously shown to bind many Wip1 substrates (RelA, p38, Chk1/2), and our results show that LZAP also binds the previously identified Wip1 substrate, MDM2. This work identifies 2 novel Wip1 substrates, ERK1 and HuR, and demonstrates that HuR is a binding partner of LZAP. Pleasingly, LZAP potentiated Wip1 catalytic activity toward each substrate tested, regardless of whether full-length substrates or phosphopeptides were utilized. Since this effect was observed on ERK1, which does not bind LZAP, as well as for each of 7 peptides tested, we hypothesize that LZAP binding to the substrate is not required for this effect and that LZAP directly binds Wip1 to augment its phosphatase activity.
Robust stability analysis of networked dynamic systems with uncertain communication delays

In this paper, we consider robust stability analysis of a networked system with uncertain communication delays. Each subsystem of these systems can have different dynamics, and interconnections among the subsystems are arbitrary. It is assumed that there exists an uncertain but constant delay in each communication channel. Based on the integral quadratic constraint (IQC) framework, a sufficient robust stability condition is derived in the form of a linear matrix inequality, which depends only on parameters of each subsystem, the subsystem connection matrix (SCM) and the selected IQC multipliers. These characteristics lead to an evident computational complexity reduction which is illustrated by some numerical results.
Characterization of the Dominant and Rare Members of a Young Hawaiian Soil Bacterial Community with Small-Subunit Ribosomal DNA Amplified from DNA Fractionated on the Basis of Its Guanine and Cytosine Composition

ABSTRACT The small-subunit ribosomal DNA (rDNA) diversity was found to be very high in a Hawaiian soil community that might be expected to have lower diversity than the communities in continental soils because the Hawaiian soil is geographically isolated and only 200 years old, is subjected to a constant climate, and harbors low plant diversity. Since an underlying community structure could not be revealed by analyzing the total eubacterial rDNA, we first fractionated the DNA on the basis of guanine-plus-cytosine (G+C) content by using bis-benzimidazole and equilibrium centrifugation and then analyzed the bacterial rDNA amplified from a fraction with a high biomass (63% G+C fraction) and a fraction with a low biomass (35% G+C fraction). The rDNA clone libraries were screened by amplified rDNA restriction analysis to determine phylotype distribution. The dominant biomass reflected by the 63% G+C fraction contained several dominant phylotypes, while the community members that were less successful (35% G+C fraction) did not show dominance but there was a very high diversity of phylotypes. Nucleotide sequence analysis revealed taxa belonging to the groups expected for the G+C contents used. The dominant phylotypes in the 63% G+C fraction were members of the Pseudomonas,Rhizobium-Agrobacterium, and Rhodospirillumassemblages, while all of the clones sequenced from the 35% G+C fraction were affiliated with several Clostridiumassemblages. The two-step rDNA analysis used here uncovered more diversity than can be detected by direct rDNA analysis of total community DNA. The G+C separation step is also a way to detect some of the less dominant organisms in a community.
Mass spectrometry‐based immuno‐precipitation proteomics – The user's guide

Immuno‐precipitation (IP) experiments using MS provide a sensitive and accurate way of characterising protein complexes and their response to regulatory mechanisms. Differences in stoichiometry can be determined as well as the reliable identification of specific binding partners. The quality control of IP and protein interaction studies has its basis in the biology that is being observed. Is that unusual protein identification a genuine novelty, or an experimental irregularity? Antibodies and the solid matrices used in these techniques isolate not only the target protein and its specific interaction partners but also many non‐specific ‘contaminants’ requiring a structured analysis strategy. These methodological developments and the speed and accuracy of MS machines, which has been increasing consistently in the last 5 years, have expanded the number of proteins identified and complexity of analysis. The European Science Foundation's Frontiers in Functional Genomics programme ‘Quality Control in Proteomics’ Workshop provided a forum for disseminating knowledge and experience on this subject. Our aim in this technical brief is to outline clearly, for the scientists wanting to carry out this kind of experiment, and recommend what, in our experience, are the best potential ways to design an IP experiment, to help identify possible pitfalls, discuss important controls and outline how to manage and analyse the large amount of data generated. Detailed experimental methodologies have been referenced but not described in the form of protocols.
Impact of continuous intraoperative neuromonitoring on autonomic nervous system during thyroid surgery

Continuous intraoperative neuromonitoring (CIONM) via vagal nerve stimulation (VNS) is a new option for recurrent laryngeal nerve (RLN) protection during thyroid surgery. The aim of this study was to evaluate the safety of VNS for CIONM and to assess its effects on the autonomic nervous system (ANS) through analyzing heart rate variability (HRV).
Glucose, glycine and diglycine in test meals at stimuli to a duodenal osmoreceptor slowing gastric emptying.

1. Five subjects took 210 test meals of 750 ml. water containing 30‐‐300 m‐molal glucose or glycine, or 15‐‐150 m‐molal diglycine, or plain water. 2. The greater the concentration of solute, the greater was the volume of original meal recovered from the stomach after a fixed time. 3. On a molal basis glucose was half as effective as diglycine in slowing gastric emptying. This was consistent with the osmoreceptor being exposed to the diglycine after it had been split by the hydrolase of the cytosol of enterocytes (the absorbing cells of the small intestine). 4. The slowing of gastric emptying (ml./mole.1.) was about 10% greater for glycine than it was for glucose. There was apparently a threshold concentration below which glycine did not slow gastric emptying. 5. It was proposed that the response of the doudenal osmoreceptor might depend upon shrinking and swelling of the lateral intercellular space around the enterocytes.
Gating of nicotinic ACh receptors: latest insights into ligand binding and function

Nicotinic acetylcholine receptors (nAChRs) are in the superfamily of cys‐loop receptors, and are widely expressed in the nervous system where they participate in a variety of physiological functions, including regulating excitability and neurotransmitter release, as well as neuromuscular contraction. Members of the cys‐loop family of receptors, which also includes the molluscan ACh‐binding protein (AChBP), a soluble protein that is analogous to the extracellular ligand‐binding domain of the cys‐loop receptors, are pentameric assemblies of five subunits, with each subunit arranged around a central pore. The binding of ACh to the extracellular interface between two subunits induces channel opening. With the recent 4 Å resolution of the Torpedo nAChR, and the crystal structure of the AChBP, much has been learned about the structure of the ligand‐binding domain and the channel pore, as well as major structural rearrangements that may confer channel opening, including a major rearrangement of the C‐loop within the ligand binding pocket, and perhaps other regions including the F‐loop (the β8–β9 linker), the β1–β2 linker and the cys‐loop. Here I will review the latest findings from my lab aimed at a further understanding of the function of the neuronal nAChR channels (and in particular the role of desensitization), and our search for novel AChBP species that may lead to a further understanding of the function of the cys‐loop receptor family.
Copy Number Variation in SOX6 Contributes to Chicken Muscle Development

Copy number variations (CNVs), which cover many functional genes, are associated with complex diseases, phenotypic diversity and traits that are economically important to raising chickens. The sex-determining region Y-box 6 (Sox6) plays a key role in fast-twitch muscle fiber differentiation of zebrafish and mice, but it is still unknown whether SOX6 plays a role in chicken skeletal muscle development. We identified two copy number polymorphisms (CNPs) which were significantly related to different traits on the genome level in chickens by AccuCopy® and CNVplex® analyses. Notably, five white recessive rock (CN = 1, CN = 3) variant individuals and two Xinghua (CN = 3) variant individuals contain a CNP13 (chromosome5: 10,500,294–10,675,531) which overlaps with SOX6. There is a disordered region in SOX6 proteins 265–579 aa coded by a partial CNV overlapping region. A quantitative real-time polymerase chain reaction showed that the expression level of SOX6 mRNA was positively associated with CNV and highly expressed during the skeletal muscle cell differentiation in chickens. After the knockdown of the SOX6, the expression levels of IGFIR1, MYF6, SOX9, SHOX and CCND1 were significantly down-regulated. All of them directly linked to muscle development. These results suggest that the number of CNVs in the CNP13 is positively associated with the expression level of SOX6, which promotes the proliferation and differentiation of skeletal muscle cells by up-regulating the expression levels of the muscle-growth-related genes in chickens as in other animal species.
FIBROPAPILLOMATOSIS IN STRANDED GREEN TURTLES (CHELONIA MYDAS) FROM THE EASTERN UNITED STATES (1980–98): TRENDS AND ASSOCIATIONS WITH ENVIRONMENTAL FACTORS

We examined data collected by the US Sea Turtle Stranding and Salvage Network on 4,328 green turtles (Chelonia mydas) found dead or debilitated (i.e., stranded) in the eastern half of the USA from Massachusetts to Texas during the period extending from 1980 to 1998. Fibropapillomatosis (FP) was reported only on green turtles in the southern half of Florida (south of 29°N latitude). Within this region, 22.6% (682/3,016) of the turtles had tumors. Fibropapillomatosis was more prevalent in turtles found along the western (Gulf) coast of Florida (51.9%) than in turtles found along the eastern (Atlantic) coast of Florida (11.9%) and was more prevalent in turtles found in inshore areas (38.9%) than in turtles found in offshore areas (14.6%). A high prevalence of FP corresponded to coastal waters characterized by habitat degradation and pollution, a large extent of shallow-water area, and low wave energy, supporting speculation that one or more of these factors could serve as an environmental cofactor in the expression of FP. A high prevalence of FP did not correspond to high-density green turtle assemblages. Turtles with tumors were found most commonly during the fall and winter months, and the occurrence of tumors was most common in turtles of intermediate size (40–70-cm curved carapace length). Stranded green turtles with tumors were more likely to be emaciated or entangled in fishing line and less likely to have propeller wounds than were stranded green turtles without tumors. Turtles with and without tumors were equally likely to show evidence of a shark attack. The percent occurrence of tumors in stranded green turtles increased from approximately 10% in the early 1980s to over 30% in the late 1990s. Fibropapillomatosis was first documented in southernmost Florida in the late 1930s and spread throughout the southern half of Florida and the Caribbean during the mid-1980s. Because green turtles living in south Florida are known to move throughout much of the Caribbean, but are not known to move to other parts of the USA or to Bermuda, the spread and current distribution of FP in the western Atlantic, Gulf of Mexico, and Caribbean can be explained by assuming FP is caused by an infectious agent that first appeared in southern Florida. Aberrant movements of captive-reared turtles or of turtles that are released into areas where they were not originally found could spread FP beyond its current distribution.
Sex‐specific linkage scans in opioid dependence

Sex influences risk for opioid dependence (OD). We hypothesized that sex might interact with genetic loci that influence the risk for OD. Therefore we performed an analysis to identify sex‐specific genomic susceptibility regions for OD using linkage. Over 6,000 single nucleotide polymorphism (SNP) markers were genotyped for 1,758 African‐ and European‐American (AA and EA) individuals from 739 families, ascertained via affected sib‐pairs with OD and/or cocaine dependence. Autosomewide non‐parametric linkage scans, stratified by sex and population, were performed. We identified one significant linkage region, segregating with OD in EA men, at 71.1 cM on chromosome 4 (LOD = 3.29; point‐wise P = 0.00005; empirical autosome‐wide P = 0.042), which significantly differed from the linkage signal at the same location in EA women (empirical P = 0.002). Three suggestive linkage signals were identified at 181.3 cM on chromosome 7 (LOD = 2.18), 104 cM on chromosome 11 (LOD = 1.85), and 60.9 cM on chromosome 16 (LOD = 1.93) in EA women. In AA men, four suggestive linkage signals were detected at 201.1 cM on chromosome 3 (LOD = 2.32), 152.9 cM on chromosome 6 (LOD = 1.86), 16.8 cM on chromosome 7 (LOD = 1.95), and 36.1 cM on chromosome 17 (LOD = 1.99). The significant region, mapping to 4q12‐4q13.1, harbors several OD candidate genes with interconnected functionality, including VEGFR, CLOCK, PDCL2, NMU, NRSF, and IGFBP7. In conclusion, these results provide an evidence for the existence of sex‐specific and population‐specific differences in OD. Furthermore, these results provide positional information that will facilitate the use of targeted next‐generation sequencing to search for genes that contribute to sex‐specific differences in OD. © 2016 Wiley Periodicals, Inc.
The Demographics of Wealth - How Age, Education and Race Separate Thrivers from Strugglers in Today's Economy. Essay No. 1: Race, Ethnicity and Wealth

Although there may be downsides to old age, those 62 and older can take heart in knowing that the odds are in favor of their being wealthier than younger people. And the gap has widened considerably over the past quarter-century? in favor of old people. That said, being old isn? t what it used to be. Baby boomers, who are now retiring in droves, are likely to be less well-off than their ? old? counterparts in the two previous generations. And it looks as if members of the next two generations ? Generation X and Generation Y (the millennials) ? might also end up less wealthy than the generation before them.
Some notes about the determination of current account equilibrium real exchange rate and the relation between real exchange rate and productive specialization

In order to do so, we will consider a small open economy that produced a homogenous good, tradable in international markets, which can be used for consumption or investment purposes. This homogenous good is supposed to be imperfect substitute of the goods produce abroad in such way that the so called law of one price is not valid. Since the economy produce just one type of good, at the same time homogenous and tradable, real exchange rate can not be defined as the ratio between the price of tradable goods to non-tradable goods; but as the ratio between
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria

Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria.
Applied aspects of data mining for decision support at the regional health system

The article presents the results of research of Data Mining methods with Microsoft SQL Server. Microsoft Clustering algorithm was used for improving the effectiveness of medical prevention and treatment in a cohort of patients with arterial hypertension. There are rationales for monitoring of cardiovascular risk and desire to correct the risk with Data Mining at medical decision support systems. Authors used medical and sociological monitoring data from regional clinical hospital. The segmentation of arterial hypertension patients was performed using Microsoft Clustering algorithm. As a result, a quantitative assessment of the population profile for patients with arterial hypertension was obtained. The authors presented diagrams and profiles of clusters. They were compared. The developed approach is applied for decision support at regional health information management system for reduce of cardiovascular risk.
Clinical significance of quantitative cytomegalovirus detection in bronchoalveolar lavage fluid in lung transplant recipients

Cytomegalovirus (CMV) is an important pathogen after lung transplant (LTx) and may be associated with bronchiolitis obliterans syndrome (BOS). We assessed the outcome of LTx patients with CMV DNA‐positive bronchoalveolar lavage (BAL) during surveillance.