Miracle-dz/UniFAR-FTUs huggingface dataset:
Incomplete X-inactivation initiated by a hypomorphic Xist allele in the mouse

X chromosome inactivation (X-inactivation) in female mammals is triggered by differential upregulation of the Xist gene on one of the two X chromosomes and subsequent coating of the X in cis with its non-coding transcripts. Although targeted mutation has clearly shown that Xist is essential for X-inactivation in cis, the molecular mechanism by which Xist RNA induces chromosome silencing is largely unknown. Here, we demonstrate that an Xist mutant generated previously in mouse by gene targeting, XistIVS, is unique in that it partially retains the capacity to silence the X chromosome. Although XistIVS is differentially upregulated and its mutated transcript coats the X chromosome in cis in embryonic and extra-embryonic tissues, X-inactivation thus initiated does not seem to be fully established. The state of such incomplete inactivation is probably unstable and the mutated X is apparently reactivated in a subset of extra-embryonic tissues and, perhaps, early epiblastic cells. XistIVS, which can be referred to as a partial loss-of-function mutation, would provide an opportunity to dissect the molecular mechanism of Xist RNA-mediated chromosome silencing.
The Sheffield language recognition system in NIST LRE 2015

The Speech and Hearing Research Group of the University of Sheffield submitted a fusion language recognition system to NIST LRE 2015. It combines three language classifiers. Two are acoustic-based, which use i–vectors and a tandem DNN language recogniser respectively. The third classifier is a phonotactic language recogniser. Two sets of training data with duration of approximately 170 and 300 hours were composed for LR training. Using the larger set of training data, the primary Sheffield LR system gives 32.44 min DCF on the official LR 2015 eval data. A post-evaluation system enhancement was carried out where i–vectors were extracted from the bottleneck features of an English DNN. The min DCF was reduced to 29.20.
User assisted stereo image segmentation

The wide availability of stereoscopic 3D displays created a considerable market for content producers. This encouraged researchers to focus on methods to alter and process the content for various purposes. This study concentrates on user assisted image segmentation and proposes a method to extend previous techniques on monoscopic image segmentation to stereoscopic footage with minimum effort. User assistance is required to indicate the representative locations of an image as object and background regions. An MRF based energy minimization technique is utilized where user inputs are applied only on one of the stereoscopic pairs. A key contribution of the proposed study is the elimination of dense disparity estimation by introducing a sparse feature matching idea. Segmentation results are evaluated by objective metrics on a ground truth stereo segmentation dataset and it can be concluded that competitive results with minimum user interaction have been obtained even without dense disparity estimation.
Acetic acid bacteria in oenology

Els bacteris de l'acid acetic han estat sempre considerats perjudicials en els ambits enologics, com a principal font de problemes en el vi (fonamentalment per ser una font d'acidesa volatil). El desenvolupament de noves tecniques de biologia molecular ha permes que la taxonomia i el coneixement del metabolisme d'aquests bacteris que, per les seves exigencies nutricionals, son molt dificils de cultivar evolucionin rapidament. En l'ambit taxonomic, s'ha produit el canvi de dos generes i cinc especies el 1984 a deu generes i mes de quaranta especies al moment actual. De totes maneres, les poderoses eines moleculars utilitzades en taxonomia no son apropiades per a l'us rutinari en estudis ecologics, on s'ha d'analitzar un gran nombre de mostres. Per tant, s'han desenvolupat noves tecniques moleculars que han permes la millora del seu coneixement i control a Enologia. Aixi mateix, han permes un avenc considerable en la produccio de vinagre, proces en el qual aquests bacteris son imprescindibles, com s'ha posat de manifest en el projecte europeu WINEGAR.
Antibiotic resistance of probiotic organisms and safety of probiotic dairy products

Intrinsic resistances to tetracycline, vancomycin and erythromycin are common in Lactobacillus species; however, resistance to streptomycin, clindamycin, gentamicin, oxacillin and lincosamide is also reported in these species. Resistant markers tet(W), tet(M) and erm(B) have been frequently detected in the resistant strains while van(A), lnu(A) and tet(L) have also been found in some strains of Lactobacillus. Bifidobacteria are commonly resistant to tetracycline, streptomycin, erythromycin, gentamicin and clindamycin. Resistance genes van(A), tet(L) and tet(M) are often detected in Enterococcus. Reports suggest enterococci to transfer tet(M) to E. faecalis or Listeria strains and van(A) to commercial strain of Lactobacillus acidophilus. Streptococcus species are highly resistant to tetracycline, ciprofloxacin and aztreonam and tet(M) was detected in strains of dairy origin. Clinical cases of endocarditis, septicemia, bacteremia and septic arthritis due to the species of Lactobacillus, Saccharomyces, Leuconostoc, Pediococcus and Bifidobacterium have been reported in patients with some underlying medical conditions.
Cumulant-based probabilistic optimal power flow (P-OPF) with Gaussian and gamma distributions

This paper introduces the cumulant method for the probabilistic optimal power flow (P-OPF) problem. By noting that the inverse of the Hessian used in the logarithmic barrier interior point can be used as a linear mapping, cumulants can be computed for unknown system variables. Results using the proposed cumulant method are compared against results from Monte Carlo simulations (MCSs) based on a small test system. The Numerical Results section is broken into two sections: The first uses Gaussian distributions to model system loading levels, and cumulant method results are compared against four MCSs. Three of the MCSs use 1500 samples, while the fourth uses 20 000 samples. The second section models the loads with a Gamma distribution. Results from the proposed technique are compared against a 1000-point MCS. The cumulant method agrees very closely with the MCS results when the mean value for variables is considered. In addition, the proposed method has significantly reduced computational expense while maintaining accuracy.
Isolation of a new foamy retrovirus from orangutans

We have isolated a new foamy virus from blood samples taken from two apparently healthy orangutans (Pongo pygmaeus). The older orangutan has since died with encephalopathy after a brief acute illness, while the younger one, his grandson, remains well. These animals and 12 other orangutans had specific antibodies to foamy virus as measured by immunofluorescence. The new foamy virus and the antisera showed strong and specific neutralization, with only weak cross-reaction with other simian foamy virus strains. Southern blotting with gag and env probes of human foamy virus and PCR amplification showed that the new foamy virus, designated SFV-11, is related to, yet distinct from, previously characterized strains from humans, chimpanzees, and monkeys.
The Mechanism of Formation of Glass-Ionomer Cement: A Theoretical Study

A resin-modified glass-ionomer cement (RMGIC) was studied from a computational point of view. We suggest terpolymer formation by reaction of fixation through a combination of acrylic acid (AA), itaconic acid (IA) and an aminoacid derivative (AAD) in different positions. We found that AAD-AA-IA is thermodynamically more stable, but AA-IA-AAD is the combination which can react with glycidyl methacrylate (GM) to form a grafted polymer with two pendant methacrylate groups which can be used later in the process of light-curing. A RMGIC contains a glass powder of calcium-fluoroaluminosilicate acting as the source of cross linking, and for this reason, we have optimized two intramolecular Al3+ tricarboxylate complexes (salt-bridges) formed from the most stable grafted polymers. A possible reaction mechanism for the addition of (GM) to copolymer is proposed.
The effect of dietary antibiotics on protein and energy metabolism in rats: possible significance of the gut microflora.

The influence of the intestinal microbial activity on protein metabolism was tested in rats with three diets fed without and with antibiotics (Nebacitin). True protein digestibility, biological value, net protein utilisation, true amino acid digestibility and apparent digestible energy were measured. The intestinal microbial activity was on average reduced to one-fifth by antibiotics. On a diet low in crude fibre (2.5%) but high in crude protein (17.6%), this reduction had only a minor influence on the parameters for protein quality that were measured. However, true digestibilities of histidine and cystine were strongly reduced by the antibiotic treatment. The digestibility of energy was also significantly reduced (5%). For diets higher in crude fibre and lower in protein, the influence of the microbial activity was more pronounced. Digestibility of protein and energy were severely reduced by the dietary antibiotic treatment. In general, antibiotic supplementation decreased the parameters that were measured.
Increased use of high-flow nasal oxygen during bronchoscopy

High-flow nasal cannula (HFNC) oxygen therapy is increasingly applied in adult patients with acute respiratory failure (ARF) [1–4]. It delivers heated and humidified air providing higher and more expected gas flow rates and fraction inspired oxygen (FiO2) than traditional oxygen therapy [2]. The patient should be clinically stable before performing bronchoscopy http://ow.ly/4mIK0W
Can the stages of change for smoking acquisition be measured reliably in adolescents?

BACKGROUND was to examine the reliability of the algorithm. METHODS As part of a randomized controlled trial, 3,930 adolescents completed a paper version of the algorithm questions and a differently worded computerized version on the same day: a parallel form reliability assessment. In a separate assessment, another group of 118 adolescents completed 2 identical paper versions of the same questionnaire 2 weeks apart: a test-retest reliability assessment. Kappa (kappa) for agreement for stage and the individual questions were calculated. Logistic regression was used to examine whether demographic characteristics, smoking status, and stage predicted agreement for stage. RESULTS Kappa (95% confidence intervals) for stage was 0.57 (0.55-0.60) in the first assessment and 0.46 (0.28-0.63) in the second assessment, indicating moderate reliability. The question concerning trying smoking in the next 6 months was moderately reliable, but that concerning trying within the next thirty days was poorly reliable. Acquisition precontemplation was significantly more reliably coded than all other stages. Demographic characteristics did not predict reliability. CONCLUSIONS The algorithm reliably allocates individuals into acquisition precontemplation, but for all other stages, its reliability is fair.
Semi-supervised k-means clustering for multi-type relational data

In many data mining tasks, there is a large supply of unlabeled data but limited labeled data since it is expensive generated. Therefore, a number of semi-supervised clustering algorithms have been proposed, but few of them are specially designed for multi-type relational data. In this paper, a semi-supervised k-means clustering algorithm for multi-type relational data is proposed, which is based on the combination of semi-supervised k-means method and multi-type relational data clustering. In order to achieve high performance, in the algorithm, we first analyze all kinds of relationships in data, which include intra-relationship, inter-relationship, explicit and implicit relationship; and then extend k-means clustering algorithm by seeding and new similarity measures, where attributes information, labeled data and all kinds of relationships are employed. The experimental results show the effectiveness of our method.
High transconductance AlGaN/GaN HEMT with thin barrier on Si(111) substrate

The fabrication of high transconductance AlGaN/GaN high electron mobility transistors (HEMTs) grown on high-resistivity silicon substrate is reported with an AlGaN barrier thickness of only 12.5 nm. A maximum DC current density of 655 mA/mm, a current gain cutoff frequency (FT) of 75 GHz and a power-gain cutoff frequency (FMAX) of 125 GHz are obtained for a 0.125 µm gate length transistor. The device provides a record peak extrinsic transconductance of 332 mS/mm and an intrinsic value of 509 mS/mm. To the authors' knowledge, the obtained transconductances are the highest reported values from AlGaN/GaN devices grown on a Si(111) substrate. This performance demonstrates the potential of GaN transistors on silicon for low-cost microwave power applications.
Sleep stage classification using the combination of SVM and PSO

Sleep quality is one of the most important factors for human physical and mental health. Sleep disorder may increase the risk of developing chronic physical and mental illnesses such as heart failure, coronary heart disease, depression, and bipolar disorder. In addition, sleep disorder also decreases work productivity and increases the risk of traffic accidents. The problem of sleep disorder is usually associated with the irregularity in sleep cycles. People need to get the right proportion of every stages and sufficient number of cycles to obtain a quality sleep. The aim of this study is to examine distinctive features related to sleep stages (wake, light sleep, deep sleep) from heart rate variability (HRV), and evaluate their usefulness to classify sleep stages. We utilize support vector machine (SVM) to classify the sleep stages classification and compare the result with conventional methods. We also utilize particle swarm optimization (PSO) for feature selection. The simulation results show that our proposed sleep classification with SVM and PSO can improve the accuracy of sleep stage classification.
A Proposed Framework for Outsourcing and Secure Encrypted Data on OpenStack Object Storage (Swift)

Despite the numerous potential benefits of Open Source Cloud Computing (OSCC) in several industrial and academic-oriented environments, OSCC could be also associated with some risks. However, which a proper awareness to the cloud consumers or organisations, these risks can be clearly identify and avoided. OpenStack Swift security can provide a greater understanding of how OpenStack Swift functions and what types of security issues arise therein. In this study, a lightweight and robust cloud-based security model for OpenStack object storage within a cloud computing environment is proposed. Swift is a multi-user based model in which every owner encrypts her/his files; each owner uses different levels of cryptographic security. A reduction in the key distribution complexity in this diverse model with a variety of security based settings is critical. Note that proposed model incorporates cryptographic algorithms at the first level (authentication/authorisation) and a hash function to introduce a more secure access method for authentication and authorisation.
Formation and Reduction of Acrylamide in Maillard Reaction: A Review Based on the Current State of Knowledge

The recent report of elevated acrylamide levels in heat processing foods evoked an international health alarm. Acrylamide, an acknowledged potential genetic and reproductive toxin with mutagenic and carcinogenic properties in experimental mammalians, has been found in various heat processing foods. Many original contributions reported their findings on the formation mechanism and possible reduction methods of acrylamide. The aim of this review article is to summarize the state-of-the-art about the formation and reduction of acrylamide in the Maillard reaction. This research progress includes mechanistic studies on the correlation between the Maillard reaction and acrylamide, the formation mechanism of acrylamide, the main pathways of formation and impact factors on formation including cultivars, storage temperature, storage time, heat temperature, heat time, environmental pH, concentration of precursors, effects of food matrixes, type of oil, etc. Meanwhile, primary mechanisms on the reduction of acrylamide as well as reduction pathways including material and processing related ways and use of exogenous chemical additives are systematically reviewed. The mitigation studies on acrylamide are also summarized by the Confederation of the Food and Drink Industries of the EU (CIAA) “Toolbox” approach.
Perspectives on Translational Biology TILLING . Traditional Mutagenesis Meets Functional Genomics

Most of the genes of an organism are known from sequence, but most of the phenotypes are obscure. Thus, reverse genetics has become an important goal for many biologists. However, reverse-genetic methodologies are not similarly applicable to all organisms. In the general strategy for reverse genetics that we call TILLING (for Targeting Induced Local Lesions in Genomes), traditional chemical mutagenesis is followed by high-throughput screening for point mutations. TILLING promises to be generally applicable. Furthermore, because TILLING does not involve transgenic modifications, it is attractive not only for functional genomics but also for agricultural applications. Here, we present an overview of the status of TILLING methodology, including Ecotilling, which entails detection of natural variation. We describe public TILLING efforts in Arabidopsis and other organisms, including maize (Zea mays) and zebrafish. We conclude that TILLING, a technology developed in plants, is rapidly being adopted in other systems.
Mechanism of Bacterial Interference with TLR4 Signaling by Brucella Toll/Interleukin-1 Receptor Domain-containing Protein TcpB*

Background: TcpB is a TIR domain-containing protein form Brucella. Results: TcpB interacts with the host Toll-like receptor and adaptors, and its structure reveals a dimer essential for activity. Conclusion: TcpB forms a nonfunctional complex with host molecules, thus suppressing signaling. Significance: The work explains the structural and functional basis of immune suppression by the protein TcpB from a pathogenic bacterium. Upon activation of Toll-like receptors (TLRs), cytoplasmic Toll/interleukin-1 receptor (TIR) domains of the receptors undergo homo- or heterodimerization. This in turn leads to the recruitment of adaptor proteins, activation of transcription factors, and the secretion of pro-inflammatory cytokines. Recent studies have described the TIR domain-containing protein from Brucella melitensis, TcpB (BtpA/Btp1), to be involved in virulence and suppression of host innate immune responses. TcpB interferes with TLR4 and TLR2 signaling pathways by a mechanism that remains controversial. In this study, we show using co-immunoprecipitation analyses that TcpB interacts with MAL, MyD88, and TLR4 but interferes only with the MAL-TLR4 interaction. We present the crystal structure of the TcpB TIR domain, which reveals significant structural differences in the loop regions compared with other TIR domain structures. We demonstrate that TcpB forms a dimer in solution, and the crystal structure reveals the dimerization interface, which we validate by mutagenesis and biophysical studies. Our study advances the understanding of the molecular mechanisms of host immunosuppression by bacterial pathogens.
rac-4-[4-Cyano-2-(hydroxymethyl)phenyl]-4-(4-fluorophenyl)-4-hydroxy-N,N-dimethylbutanaminium hemifumarate

In the title salt, C20H24FN2O2 +·0.5C4H2O4 2−, the fumarate anion is located on an inversion centre. In the cation, the two benzene rings are nearly perpendicular to each other, making a dihedral angle of 87.41 (10)°. The cation is linked to the anion by a bifurcated N—H⋯O hydrogen bond. Classical O—H⋯O and weak C—H⋯F hydrogen bonding is also present in the crystal structure. Three C atoms of the N,N-dimethylbutanaminium moiety are disordered over two sites with refined site occupancies of 0.466 (14) and 0.534 (14).
Patellar position in weight-bearing radiographs compared with non-weight-bearing: significance for the detection of osteoarthritis

Background Diagnosis and treatment of patellofemoral disorders including osteoarthritis are currently often based on imaging and clinical assessment with patients in the supine position. Purpose To evaluate differences in patellar position in the trochlear groove and to assess the detection of medial and lateral patellofemoral (PF) osteoarthritis (OA) on axial radiographs in supine and standing positions, respectively. Material and Methods Thirty-five women and 23 men (mean age, 56 years; age range, 18–87 years) referred for routine radiographic examinations of the knees were included. Axial radiographs of the PF joint in both supine non-weight-bearing and standing weight-bearing position in 30° knee flexion were obtained of 111 knees. Measurements performed on the radiographs: patellar tilt, patellar displacement, joint space width, and grade of OA according to Ahlbäck. Results From supine to standing position the patella moved medially and medial joint space width and lateral patellar tilt angle decreased (P < 0.0001 for the three measured parameters). In the standing position, medial PF OA was observed in 19 knees compared to three knees in the supine position. Fourteen knees had lateral PF OA with almost unchanged grade of OA irrespective of position. Conclusion In weight-bearing positions, the patella is positioned medially in the trochlear groove compared to supine non-weight-bearing positions. Therefore, this study suggests that the common occurrence of medial PF OA can generally not be detected on axial radiographs in supine non-weight-bearing positions and confirms the importance of imaging the PF joint in standing weight-bearing positions.
Experimental anti-tumor therapy in 3-D: Spheroids – old hat or new challenge?

Purpose: To give a state-of-the-art overview on the promise of three-dimensional (3-D) culture systems for anticancer drug development, with particular emphasis on multicellular tumor spheroids (MCTS). Results and conclusions: Cell-based assays have become an integral component in many stages of routine anti-tumor drug testing. However, they are almost always based on homogenous monolayer or suspension cultures and thus represent a rather artificial cellular environment. 3-D cultures – such as the well established spheroid culture system – better reflect the in vivo behavior of cells in tumor tissues and are increasingly recognized as valuable advanced tools for evaluating the efficacy of therapeutic intervention. The present article summarizes past and current applications and particularly discusses technological challenges, required improvements and recent progress with the use of the spheroid model in experimental therapeutics, as a basis for sophisticated drug/therapy screening. A brief overview is given focusing on the nomenclature of spherical 3-D cultures, their potential to mimic many aspects of the pathophysiological situation in tumors, and currently available protocols for culturing and analysis. A list of spheroid-forming epithelial cancer cell lines of different origin is provided and the recent trend to use spheroids for testing combination treatment strategies is highlighted. Finally, various spheroid co-culture approaches are presented that have been established to study heterologous cell interactions in solid tumors and thereby are able to reflect the cellular tumor environment with increasing accuracy. The intriguing observation that in order to retain certain tumor initiating cell properties, some primary tumor cell populations must be maintained exclusively in 3-D culture is mentioned, adding a new but fascinating challenge for future therapeutic campaigns.