Miracle-dz/UniFAR-FTUs huggingface dataset:
Fermentation of Glucose, Lactose, Galactose, Mannitol, and Xylose by Bifidobacteria

For six strains of Bifidobacterium bifidum (Lactobacillus bifidus), fermentation balances of glucose, lactose, galactose, mannitol, and xylose were determined. Products formed were acetate, l(+)-lactate, ethyl alcohol, and formate. l(+)-Lactate dehydrogenase of all strains studied was found to have an absolute requirement for fructose-1,6-diphosphate. The phosphoroclastic enzyme could not be demonstrated in cell-free extracts. Cell suspensions fermented pyruvate to equimolar amounts of acetate and formate. Alcohol dehydrogenase was shown in cell-free extracts. Possible explanations have been suggested for the differences in fermentation balances found for different strains and carbon sources. By enzyme determinations, it was shown that bifidobacteria convert mannitol to fructose-6-phosphate by an inducible polyol dehydrogenase and fructokinase. For one strain of B. bifidum, molar growth yields of glucose, lactose, galactose, and mannitol were determined. The mean value of Y (ATP), calculated from molar growth yields and fermentation balances, was 11.3.
Hydrogel-based electrochemical sensor for non-invasive and continuous glucose monitoring

Monitoring blood glucose level of diabetic patients is crucial in diabetes care from life threating complications. Selfmonitoring blood glucose (SMBG) that involves finger prick to draw blood samples into the measurement system is a widely-used method of routine measurement of blood glucose levels to date. SMBG includes, however, unavoidable pain problems resulting from the repetitive measurements. We hereby present a hydrogel-based electrochemical (H-EC) sensor to monitor the glucose level, non-invasively. Glucose oxidase (GOx) was immobilized in the disc-type hydroxyethyl methacrylate (HEMA) based hydrogel and kept intact in the hydrogel. Fast electron transfer mediated by Prussian blue (PB, hexacyanoferrate) generated efficient signal amplifications to facilitate the detection of the extracted glucose from the interstitial fluid. The linear response and the selectivity against glucose of the H-EC sensor were validated by chronoamperometry. For the practical use, the outcomes from the correlation of the extracted glucose concentration and the blood glucose value by on-body extraction, as well as the validation of the hydrogel-based electrochemical (H-EC) device, were applied to the on-body glucose monitoring.
Accurately annotate compound effects of genetic variants using a context-sensitive framework

Abstract In genomics, effectively identifying the biological effects of genetic variants is crucial. Current methods handle each variant independently, assuming that each variant acts in a context-free manner. However, variants within the same gene may interfere with each other, producing combinational (compound) rather than individual effects. In this work, we introduce COPE, a gene-centric variant annotation tool that integrates the entire sequential context in evaluating the functional effects of intra-genic variants. Applying COPE to the 1000 Genomes dataset, we identified numerous cases of multiple-variant compound effects that frequently led to false-positive and false-negative loss-of-function calls by conventional variant-centric tools. Specifically, 64 disease-causing mutations were identified to be rescued in a specific genomic context, thus potentially contributing to the buffering effects for highly penetrant deleterious mutations. COPE is freely available for academic use at http://cope.cbi. pku.edu. cn.
Identification of Acidic Dileucine Signals in LRP9 that Interact with Both GGAs and AP‐1/AP‐2

The Golgi‐localized, gamma‐ear‐containing, ADP ribosylation factor‐binding family of monomeric clathrin adaptors (GGAs) is known to bind cargo molecules through short C‐terminal peptide motifs conforming to the sequence DXXLL (X = any amino acid), while the heterotetrameric adaptors AP‐1 and AP‐2 utilize a similar but discrete sorting motif of the sequence [D,E]XXXL[L,I]. While it has been established that a single cargo molecule may contain either or both types of these acidic cluster‐dileucine (AC‐LL) sorting signals, there are no examples of cargo with overlapping GGA and AP‐1/AP‐2‐binding motifs. In this study, we report that the cytosolic tail of low‐density lipoprotein receptor‐related protein (LRP)9 contains a bifunctional GGA and AP‐1/AP‐2‐binding motif at its carboxy‐terminus (EDEPLL). We further demonstrate that the internal EDEVLL sequence of LRP9 also binds to GGAs in addition to AP‐2. Either AC‐LL motif of LRP9 is functional in endocytosis. These findings represent the first study characterizing the trafficking of LRP9 and also have implications for the identification of additional GGA cargo molecules.
Resource allocation for the multi-cell OFDMA system and its capacity bounds

Recently, joint subchannel allocation and transmission power control problems for multi-cell orthogonal frequency-division multiple access (OFDMA) systems have been actively studied. However, since the problems are notoriously difficult and complex, only heuristic approaches are mainly used to study the problems without trying to achieve the optimal resource allocation and the maximum system capacity. In this paper, we study the joint subchannel allocation and transmission power control problem for multi-cell OFDMA systems from the point of the optimal resource allocation and the maximum system capacity with a monotonic optimization approach. Even though we do not obtain the exact optimal resource allocation that achieves the maximum system capacity, we develop an algorithm for resource allocations that provide both upper and lower bounds on the maximum system capacity. Through numerical results, we evaluate our algorithm showing that it provides good approximations to the maximum system capacity in multi-cell OFDMA systems in most cases.
Dexamethasone potentiates myeloid‐derived suppressor cell function in prolonging allograft survival through nitric oxide

Whereas GCs have been demonstrated to be beneficial for transplantation patients, the pharmacological mechanisms remain unknown. Herein, the role of GR signaling was investigated via a pharmacological approach in a murine allogeneic skin transplantation model. The GC Dex, a representative GC, significantly relieved allograft rejection. In Dex‐treated allograft recipient mice, CD11b+Gr1+ MDSCs prolonged graft survival and acted as functional suppressive immune modulators that resulted in fewer IFN‐γ‐producing Th1 cells and a greater number of IL‐4‐producing Th2 cells. In agreement, Dex‐treated MDSCs promoted reciprocal differentiation between Th1 and Th2 in vivo. Importantly, the GR is required in the Dex‐induced MDSC effects. The blocking of GR with RU486 significantly diminished the expression of CXCR2 and the recruitment of CD11b+Gr1+ MDSCs, thereby recovering the increased MDSC‐suppressive activity induced by Dex. Mechanistically, Dex treatment induced MDSC iNOS expression and NO production. Pharmacologic inhibition of iNOS completely eliminated the MDSC‐suppressive function and the effects on T cell differentiation. This study shows MDSCs to be an essential component in the prolongation of allograft survival following Dex or RU486 treatment, validating the GC–GR–NO signaling axis as a potential therapeutic target in transplantation.
Clinical Depression and Regulation of the Inflammatory Response During Acute Stress

Objective: This study examined whether clinical depression is associated with a differential inflammatory response to an acute bout of psychological stress. Methods: A total of 72 women participated in the study; half met diagnostic criteria for clinical depression; the others had no history of psychiatric illness. The groups were matched with respect to age and ethnicity. All subjects were exposed to a 17-minute mock-job interview; blood was drawn to assess secretion and regulation of inflammatory molecules. Results: The stressor was associated with feelings of shame and anxiety, a mobilization of monocytes, neutrophils, and C-reactive protein into the circulation, and greater endotoxin-stimulated production of interluekin-6 and tumor necrosis factor-&agr; by white blood cells in vitro. Depressed subjects began the session with greater sensitivity to the antiinflammatory properties of glucocorticoids than control subjects. Following exposure to the stressor protocol, however, sensitivity decreased among depressed subjects and increased among controls. This was manifest by disparities in interluekin-6 and tumor necrosis factor-&agr; production in the presence of dexamethasone. Conclusions: These findings suggest that under acutely challenging conditions, depression is associated with greater resistance to molecules that normally terminate the inflammatory cascade. An impaired capacity to regulate inflammation could underlie some of the excess morbidity and mortality that has been associated with depression. IL-6 = interleukin-6; TNF-&agr; = tumor necrosis factor-&agr;; IC50 = 50% inhibitory concentration; LPS = lipopolysaccharide.
Galaxy Zoo: bulgeless galaxies with growing black holes

The growth of supermassive black holes appears to be driven by galaxy mergers, violent merger-free processes and/or ‘secular’ processes. In order to quantify the effects of secular evolution on black hole growth, we study a sample of active galactic nuclei (AGN) in galaxies with a calm formation history free of significant mergers, a population that heretofore has been difficult to locate. Here we present an initial sample of 13 AGN in massive (M* ≳ 1010 M⊙) bulgeless galaxies – which lack the classical bulges believed inevitably to result from mergers – selected from the Sloan Digital Sky Survey using visual classifications from Galaxy Zoo. Parametric morphological fitting confirms that the host galaxies lack classical bulges; any contributions from pseudo-bulges are very small (typically <5 per cent). We compute black hole masses for the two broad-line objects in the sample (4.2 × 106 and 1.2 × 107 M⊙) and place lower limits on black hole masses for the remaining sample (typically MBH ≳ 106 M⊙), showing that significant black hole growth must be possible in the absence of mergers or violent disc instabilities. The black hole masses are systematically higher than expected from established bulge–black hole relations. However, if the mean Eddington ratio of the systems with measured black hole masses (L/LEdd ≈ 0.065) is typical, 10 of 13 sources are consistent with the correlation between black hole mass and total stellar mass. That pure disc galaxies and their central black holes may be consistent with a relation derived from elliptical and bulge-dominated galaxies with very different formation histories implies the details of stellar galaxy evolution and dynamics may not be fundamental to the co-evolution of galaxies and black holes.
Evaluation of widely used models for predicting BRCA1 and BRCA2 mutations

Deleterious mutations of the BRCA1 and BRCA2 genes are a major risk factor for the development of breast and ovarian cancers.1–4 Mutation tests for these two genes commonly are now offered in specialised clinics.5,6 As a result, a large number of women with personal or family histories of breast or ovarian cancer seek genetic counselling. Accurate evaluation of the probability that a woman carries a germline pathogenic mutation at BRCA1 or BRCA2 therefore is essential to help counsellors and those being counselled to decide whether testing is appropriate. In this context, the questions of practical interest are: Given the pedigree, what is the chance of a mutation being present? and What is the chance of the DNA laboratory finding a mutation? After testing became available, several models were developed to assess the pre-test probability of identifying carriers of mutations. Broadly speaking, two different approaches have been used to develop predictive models: the “empirical approach” and the “Mendelian approach”. 7 In empirical models, families are stratified according to variables that describe their family history; regression or other approaches are used to predict the results of Mendelian testing. In some cases, this approach simply consists of observing the proportion of mutations found in different strata. Mendelian models, in contrast, address the probability that a proband is a mutation carrier on the basis of explicit assumptions about the genetic parameters (allele frequencies and cancer penetrances in carriers and non-carriers) and the Mendelian rules of gene transmission. A consequence of the two different strategies is that the Mendelian models evaluate the probability that a proband is a gene carrier, whereas the empirical models evaluate the probability of identifying a mutation. The main purpose of this study was to compare the performances of published models in predicting mutation test results in …
Symptom dimensions and subtypes of obsessive-compulsive disorder: a developmental perspective

In the absence of definitive etiological markers for obsessive-compulsive disorder (OCD), obsessive-compulsive (OC) symptom dimensions may offer a fruitful point of orientation. These dimensions can be understood as defining potentially overlapping clinical features that may be continuous with “normal” worries first evident in childhood. Although the understanding of the dimensional structure of OC symptoms is still imperfect, a recent large-scale meta-analysis has confirmed the presence of at least four separable symptom dimensions in children, as well as adults, with OCD, A dimensional approach does not exclude other methods to parse OCD. Thus far, a pediatric age of onset, the presence of other family members with OCD, and the individual's “ticrelated” status appear to be potentially useful categorical distinctions. Although the OC symptom dimensions appear to be valid for all ages, it is unlikely that the underlying genetic vulnerability factors and neurobiological substrates for each of these symptom dimensions are the same across the course of development.
Mining Apps for Abnormal Usage of Sensitive Data

What is it that makes an app malicious? One important factor is that malicious apps treat sensitive data differently from benign apps. To capture such differences, we mined 2,866 benign Android applications for their data flow from sensitive sources, and compare these flows against those found in malicious apps. We find that (a) for every sensitive source, the data ends up in a small number of typical sinks; (b) these sinks differ considerably between benign and malicious apps; (c) these differences can be used to flag malicious apps due to their abnormal data flow; and (d) malicious apps can be identified by their abnormal data flow alone, without requiring known malware samples. In our evaluation, our MUDFLOW prototype correctly identified 86.4% of all novel malware, and 90.1% of novel malware leaking sensitive data.
Detection of G12 Human Rotaviruses in Nepal

Of 731 stool specimens collected from children with diarrhea in Kathmandu, Nepal, from August 2004 through July 2005, 170 (23.3%) tested positive for rotavirus. Reverse transcription–PCR, including a revised G12-specific primer set, identified 56 (32.9%) as G2P[4] and 39 (23.0%) as G12 with P[6], P[8], or P[4].
Cell Wall N-Linked Mannoprotein Biosynthesis Requires Goa1p, a Putative Regulator of Mitochondrial Complex I in Candida albicans

The Goa1p of Candida albicans regulates mitochondrial Complex I (CI) activities in its role as a putative CI accessory protein. Transcriptional profiling of goa1∆ revealed a down regulation of genes encoding β-oligomannosyl transferases. Herein, we present data on cell wall phenotypes of goa1∆ (strain GOA31). We used transmission electron microscopy (TEM), GPC/MALLS, and NMR to compare GOA31 to a gene-reconstituted strain (GOA32) and parental cells. We note by TEM a reduction in outer wall fibrils, increased inner wall transparency, and the loss of a defined wall layer close to the plasma membrane. GPC-MALLS revealed a reduction in high and intermediate Mw mannan by 85% in GOA31. A reduction of β-mannosyl but not α-mannosyl linkages was noted in GOA31 cells. β-(1,6)-linked glucan side chains were branched about twice as often but were shorter in length for GOA31. We conclude that mitochondrial CI energy production is highly integrated with cell wall formation. Our data also suggest that not all cell wall biosynthetic processes are dependent upon Goa1p even though it provides high levels of ATP to cells. The availability of both broadly conserved and fungal-specific mutants lacking CI subunit proteins should be useful in assessing functions of fungal-specific functions subunit proteins.
B- AND A-TYPE STARS IN THE TAURUS–AURIGA STAR-FORMING REGION

We describe the results of a search for early-type stars associated with the Taurus–Auriga molecular cloud complex, a diffuse nearby star-forming region noted as lacking young stars of intermediate and high mass. We investigate several sets of possible O, B, and early A spectral class members. The first is a group of stars for which mid-infrared images show bright nebulae, all of which can be associated with stars of spectral-type B. The second group consists of early-type stars compiled from (1) literature listings in SIMBAD, (2) B stars with infrared excesses selected from the Spitzer Space Telescope survey of the Taurus cloud, (3) magnitude- and color-selected point sources from the Two Micron All Sky Survey, and (4) spectroscopically identified early-type stars from the Sloan Digital Sky Survey coverage of the Taurus region. We evaluated stars for membership in the Taurus–Auriga star formation region based on criteria involving: spectroscopic and parallactic distances, proper motions and radial velocities, and infrared excesses or line emission indicative of stellar youth. For selected objects, we also model the scattered and emitted radiation from reflection nebulosity and compare the results with the observed spectral energy distributions to further test the plausibility of physical association of the B stars with the Taurus cloud. This investigation newly identifies as probable Taurus members three B-type stars: HR 1445 (HD 28929), τ Tau (HD 29763), 72 Tau (HD 28149), and two A-type stars: HD 31305 and HD 26212, thus doubling the number of stars A5 or earlier associated with the Taurus clouds. Several additional early-type sources including HD 29659 and HD 283815 meet some, but not all, of the membership criteria and therefore are plausible, though not secure, members.
Efficient Multi-Dimensional Flow Correlation

Flow correlation algorithms compare flows to determine similarity, and are especially useful and well studied for detecting flow chains through "stepping stone" hosts. Most correlation algorithms use only one characteristic and require all values in the correlation matrix (the correlation value of all flows to all other flows) to be updated on every event. We have developed an algorithm that tracks multiple (n) characteristics per flow, and requires updating only the flow's n values upon an event, not all the values for all the flows. The n correlation values are used as coordinates for a point in n-space; two flows are considered correlated if there is a very small Euclidean distance between them. Our results show that this algorithm is efficient in space and compute time, is resilient against anomalies in the flow, and has uses outside of stepping stone detection.
Precordial and Epicardial Surface Potentials during Myocardial Ischemia in the Pig: A THEORETICAL AND EXPERIMENTAL ANALYSIS OF THE TQ AND ST SEGMENTS

The solid angle theorem was used to analyze the relationships between TQ and ST segment deflections recorded from precordial and epicardial locations and the time course, size, shape, and transmural location of the ischemic process in the ventricular myocardium. Mathematical predictions were compared with experimental data from the intact heart. Precordial electrograms obtained in anesthetized close-chest pigs were compared with epicardial electrograms recorded directly from the heart's surface. Various areas of ischemia were produced by occluding large and small coronary artery branches, and the resultant changes in ischemic shape were delineated with Thioflavin S injections and postmortem ultraviolet photography. Formally derived equations and cumulative experimental data were in close agreement, suggesting that in the ischemic ventricle (1) TQ depression always accompanies ST elevation, (2) TQ and ST segment changes in magnitude and polarity are complex functions of ischemic size, shape, and transmural location; (3) precordial electrocardiogram (ECG) ST segment elevation is directly related to ischemic size; and (4) epicardial ECG ST segment elevation is inversely related to ischemic size. It is thus concluded that precordial and epicardial ECG TQ and ST segment deflections are complex functions of ischemic geometry and that their accurate interpretation with respect to ischemic size and shape and in the presence of pharmacological interventions is often difficult and may be misleading.
Yeast MAK3 N-acetyltransferase recognizes the N-terminal four amino acids of the major coat protein (gag) of the L-A double-stranded RNA virus

The MAK3 gene of Saccharomyces cerevisiae encodes an N-acetyltransferase whose acetylation of the N terminus of the L-A double-stranded RNA virus major coat protein (gag) is necessary for viral assembly. We show that the first 4 amino acids of the L-A gag protein sequence, MLRF, are a portable signal for N-terminal acetylation by MAK3. Amino acids 2, 3, and 4 are each important for acetylation by the MAK3 enzyme. In yeast cells, only three mitochondrial proteins are known to have the MAK3 acetylation signal, suggesting an explanation for the slow growth of mak3 mutants on nonfermentable carbon sources.
Particle Shape Factors and Their Use in Image Analysis – Part 1 : Theory

INTRODUCTION Fine particle characterization is most effective when accomplished through a methodical process. The first step of this process often involves determining what material needs characterization. In general, the following instances are most often cited: • When a new chemical entity or active pharmaceutical ingredient is identified • When the production of an existing substance is changed (e.g., new salt form established, recrystalization process changed, milling parameters altered, etc.) • When there exists two lots or batches of virtually identical material that behave differently in some manner.
Asymptotic density and computably Enumerable Sets

We study connections between classical asymptotic density and c.e. sets. We prove that a c.e. Turing degree d is not low if and only if d contains a c.e. set A of density 1 which has no computable subsets of density 1, giving a natural characterization of non-low c.e. degrees. In contrast, we prove that every nonzero c.e. degree contains a set which is generically computable but not coarsely computable. There is a very close connection between the computational complexity of a set and the computational complexity of its density as a real number where we measure complexity of real numbers as the position of their left Dedekind cuts in the Arithmetic Hierarchy. We characterize the lower densities, upper densities and densities of both computable and computably enumerable sets. We also study "computable at density r" where r is an arbitrary real number in the unit interval. Finally, we study connections between density and classical smallness notions such as immunity and cohesiveness.