Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of Stress-Strain and Shock Bump Hazard of Rock Mass in the Zones of High-Amplitude Tectonic Dislocations

The paper analyses geodynamic processes in the development of the Talnakh and Oktyabrsk deposits, which have complex geological structure. It demonstrates the results of the forecast estimation of seismic energy released on the contact surface of the fault plane of type I and II tectonic dislocations when stoping approaches. The article discusses the geodynamic processes occurring during the mining of the Talnakh and Oktyabrsky deposits of complex geological structure. The results of predictive assessments of seismic energy released at the contact surface displacement of a tectonic disturbance type I and II at the approach of remediation. For practical use of the obtained graph of the dependence of critical distance from the front of the treatment works to a tectonic disturbance on the magnitude of the angle of internal friction.
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.
Rankine‐Hugoniot Relations in Multispecies Plasma With Gyrotropic Anisotropic Downstream Ion Distributions

In the observed heliospheric shocks downstream distributions are usually measured in the regions where the kinematic relaxation has already happened but isotropy is not achieved. Rankine‐Hugoniot relations, connecting the upstream and downstream plasma parameters, should be able to take into account the downstream ion anisotropy. In a multispecies plasma different species behave differently at the ramp crossing and when collisionlessly gyrating in the downstream region. The downstream density and pressure of each species can be expressed in terms of the magnetic compression and the cross‐shock potential, which allows us to derive new Rankine‐Hugoniot relations.
Expansions and eigenfrequencies for damped wave equations

We study eigenfrequencies and propagator expansions for damped wave equations on compact manifolds. In the strongly damped case, the propagator is shown to admit an expansion in terms of the finitely many eigenmodes near the real axis, with an error exponentially decaying in time. In the presence of an elliptic closed geodesic not meeting the support of the damping coefficient, we show that there exists a sequence of eigenfrequencies converging rapidly to the real axis. In the case of Zoll manifolds, the set of all eigenfrequencies is shown to exhibit a cluster structure determined by the Morse index of the closed geodesics and the damping coefficient averaged along the geodesic flow. We then show that the propagator can be expanded in terms of the clusters of eigenfrequencies in the entire spectral band.
Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease

Kawasaki disease (KD) is a systemic vasculitis of unknown etiology. Absence of definitive diagnostic markers limits the accuracy of clinical evaluations of suspected KD with significant increases in morbidity. In turn, incomplete understanding of its molecular pathogenesis hinders the identification of rational targets needed to improve therapy. We used high‐accuracy mass spectrometry proteomics to analyse over 2000 unique proteins in clinical urine specimens of patients with KD. We discovered that urine proteomes of patients with KD, but not those with mimicking conditions, were enriched for markers of cellular injury such as filamin and talin, immune regulators such as complement regulator CSMD3, immune pattern recognition receptor muclin, and immune cytokine protease meprin A. Significant elevations of filamin C and meprin A were detected in both the serum and urine in two independent cohorts of patients with KD, comprised of a total of 236 patients. Meprin A and filamin C exhibited superior diagnostic performance as compared to currently used markers of disease in a blinded case‐control study of 107 patients with suspected KD, with receiver operating characteristic areas under the curve of 0.98 (95% confidence intervals [CI] of 0.97–1 and 0.95–1, respectively). Notably, meprin A was enriched in the coronary artery lesions of a mouse model of KD. In all, urine proteome profiles revealed novel candidate molecular markers of KD, including filamin C and meprin A that exhibit excellent diagnostic performance. These disease markers may improve the diagnostic accuracy of clinical evaluations of children with suspected KD, lead to the identification of novel therapeutic targets, and allow the development of a biological classification of Kawasaki disease.
Analysis of Wilms Tumors Using SNP Mapping Array-Based Comparative Genomic Hybridization

Wilms tumor (WT) has been a model to study kidney embryogenesis and tumorigenesis and, although associated with hereditary, cancer predisposition syndromes, the majority of tumors occur sporadically. To analyze genetic changes in WT we have defined copy number changes and loss of heterozygosity in 56 Wilms tumors using high resolution oligonucleotide arrays at a average resolution of ∼12 Kb. Consistent deletions were seen on chromosomes 1p, 4q, 7p, 9q, 11p, 11q, 14q, 16q, and 21q. High frequency gains were seen for 1q and lower frequency gains were seen on 7q and chromosomes 8, 12 and 18. The high resolution provided by the SNP mapping arrays has defined minimal regions of deletion for many of these LOH events. Analysis of CNAs by tumor stage show relatively stable karyotypes in stage 1 tumors and more complex aCGH profiles in tumors from stages 3–5.
Corticosteroids and the risk of atrial fibrillation.

BACKGROUND High-dose (pulse) corticosteroid therapy has been associated with the development of atrial fibrillation. This association, however, is mainly based on case reports. METHODS To test the hypothesis that high-dose corticosteroid exposure increases the risk of new-onset atrial fibrillation, we performed a nested case-control study within the Rotterdam Study, a population-based cohort study among 7983 older adults. Cases were defined as persons with incident atrial fibrillation between July 1, 1991, and January 1, 2000. Their date of diagnosis was defined as the index date. All noncases within the Rotterdam Study who were alive and eligible on this index date were used as controls. Subsequently, we compared the proportion of cases and controls that received a corticosteroid prescription within 1 month preceding the index date. Corticosteroid exposure was categorized into high-dose exposure (oral or parenteral steroid at a daily dose > or =7.5 mg of prednisone equivalents) and low-intermediate-dose exposure (<7.5 mg of prednisone equivalents or inhaled corticosteroids). RESULTS There were 385 eligible cases of new-onset atrial fibrillation during the study period. The risk of new-onset atrial fibrillation was significantly higher for persons who received a corticosteroid prescription within 1 month before the index date than for those without (odds ratio [OR], 3.75; 95% confidence interval [CI], 2.38-5.87). However, only high-dose corticosteroid use was associated with an increased risk (OR, 6.07; 95% CI, 3.90-9.42), whereas low-intermediate-dose use was not (OR, 1.42; 95% CI, 0.72-2.82). The association of atrial fibrillation with high-dose corticosteroid use was largely independent of the indication for corticosteroid therapy, since the risk of new-onset atrial fibrillation was not only increased in patients with asthma or chronic obstructive pulmonary disease (OR, 4.02; 95% CI, 2.07-7.81) but also in patients with rheumatic, allergic, or malignant hematologic diseases (OR, 7.90; 95% CI, 4.47-13.98). CONCLUSION Our findings strongly suggest that patients receiving high-dose corticosteroid therapy are at increased risk of developing atrial fibrillation.
Effect of the physico-chemical parameters on the distribution of the fecal flora in a dam reservoir (Algeria)

RÉSUMÉ. — Effet des paramètres physico-chimiques sur la distribution de la flore fécale dans un barrage (Algérie). — La présente étude a été effectuée en vue d’évaluer l’influence des fluctuations des paramètres environnementaux sur la charge et la distribution des différentes populations bactériennes d’origine fécale dans le barrage de Boukourdane (Algérie). Le suivi a été établi pendant deux ans (janvier 2013 – janvier 2015) au niveau de quatre stations. Le dénombrement des germes fécaux a été effectué en surface et en profondeur. Le suivi des paramètres bactériologiques a révélé une variation saisonnière, les charges bactériennes enregistrées sont assez élevées surtout durant les saisons froides (hiver et automne). L’analyse canonique de correspondances (ACC) de l’ensemble des données obtenues fait apparaître le rôle significatif de la conductivité, des ortho-phosphates et du pH sur le développement des streptocoques fécaux. L’ACC montre également l’effet des variations saisonnières et des ions sulfates sur la répartition des anaérobies sulfito-réducteurs. Concernant les coliformes totaux ils sont liés à la température de l’eau et les coliformes fécaux aux ions nitrates et à l’oxygène dissous.
Different Consequences of ACE2 and SWI5 Gene Disruptions for Virulence of Pathogenic and Nonpathogenic Yeasts

ABSTRACT Mutants of Candida albicans, Candida glabrata, and Saccharomyces cerevisiae with disruptions in the ACE2 gene and C. glabrata and S. cerevisiae swi5 disruption mutants were tested for virulence in a murine challenge model of disseminated yeast infection. All mutants showed a clumping phenotype, but clumping was minimized in challenge inocula by inclusion of chitinase in the growth medium. In animals rendered temporarily neutropenic by cyclophosphamide treatment, the C. glabrata ace2 null mutant was confirmed as hypervirulent: it led to early terminal illness and kidney, brain, and lung fungal burdens substantially and significantly larger than those in controls. The C. glabrata swi5 null mutant did not lead to terminal illness but generated significantly larger brain and lung burdens than those in controls. The C. albicans ace2 null mutant was very slightly attenuated and the S. cerevisiae ace2 and swi5 null mutants were substantially attenuated relative to their parental control strains. The phenotype of aggressive hypervirulence, unique to disruption of the C. glabrata ACE2 gene among the strains tested, was not seen when the C. glabrata ace2 strain was tested in immunologically intact mice. The different effects seen with these mutants rule out the clumping phenotype as the explanation for hypervirulence in the C. glabrata ace2 mutant. The absence of C. glabrata ace2 hypervirulence in healthy mice may be a tool for definitive future study of host-parasite cross talk in microbial opportunism.
NadA, a Novel Vaccine Candidate of Neisseria meningitidis

Neisseria meningitidis is a human pathogen, which, in spite of antibiotic therapy, is still a major cause of mortality due to sepsis and meningitis. Here we describe NadA, a novel surface antigen of N. meningitidis that is present in 52 out of 53 strains of hypervirulent lineages electrophoretic types (ET) ET37, ET5, and cluster A4. The gene is absent in the hypervirulent lineage III, in N. gonorrhoeae and in the commensal species N. lactamica and N. cinerea. The guanine/cytosine content, lower than the chromosome, suggests acquisition by horizontal gene transfer and subsequent limited evolution to generate three well-conserved alleles. NadA has a predicted molecular structure strikingly similar to a novel class of adhesins (YadA and UspA2), forms high molecular weight oligomers, and binds to epithelial cells in vitro supporting the hypothesis that NadA is important for host cell interaction. NadA induces strong bactericidal antibodies and is protective in the infant rat model suggesting that this protein may represent a novel antigen for a vaccine able to control meningococcal disease caused by three hypervirulent lineages.
ERCP-related perforations in the new millennium: A large tertiary referral center 10-year experience

Introduction Endoscopic retrograde cholangiopancreatography (ERCP) is an important diagnostic and therapeutic modality for pancreatic and biliary disorders. Perforation is one of the most dreaded complications of ERCP. Since it is uncommon, there has been little study of incidence, risk factors, and outcomes of management. Objectives We aim to assess the incidence of ERCP-related perforations and outcomes at a large tertiary referral center. Methods We undertook a review of an ERCP database for all perforations from 2002 to December 2012. Results The cumulative incidence of ERCP-related perforations was 0.14% (12 out of 8264), and sphincterotomy-related perforations constituted the most common cause. The mean age of these 12 patients was 58.6 years and majority were female (83.3%). The most common indications for ERCP were: suspected sphincter of Oddi dysfunction (SOD) 41%, and common bile duct stones (CBD stones) 41%. Nine of the 12 patients (75%) had a leak and were managed medically, and four who had a perforation had surgical repair (25%). Conclusions In our study, leaks were much more common than perforations and the majority of patients were successfully managed with conservative therapy alone. We report a very low perforation rate and most perforations can be managed conservatively with a good outcome.
Autophagic Tubes

Many intracellular compartments of eukaryotic cells do not adopt a spherical shape, which would be expected in the absence of mechanisms organizing their structure. However, little is known about the principles determining the shape of organelles. We have observed very defined structural changes of vacuoles, the lysosome equivalents of yeast. The vacuolar membrane can form a large tubular invagination from which vesicles bud off into the lumen of the organelle. Formation of the tube is regulated via the Apg/Aut pathway. Its lumen is continuous with the cytosol, making this inverse budding reaction equivalent to microautophagocytosis. The tube is highly dynamic, often branched, and defined by a sharp kink of the vacuolar membrane at the site of invagination. The tube is formed by vacuoles in an autonomous fashion. It persists after vacuole isolation and, therefore, is independent of surrounding cytoskeleton. There is a striking lateral heterogeneity along the tube, with a high density of transmembrane particles at the base and a smooth zone devoid of transmembrane particles at the tip where budding occurs. We postulate a lateral sorting mechanism along the tube that mediates a depletion of large transmembrane proteins at the tip and results in the inverse budding of lipid-rich vesicles into the lumen of the organelle.
A method to construct complementary sets of non-power-of-two length by concatenation

The existing constructions of Golay complementary sets based on generalized Boolean functions are limited to lengths, which are powers of two. In a recent paper, Chen [3] proposed a new construction of binary and nonbinary complementary sets of non-power-of-two length based on truncated method. In this paper, we proposed a novel construction of ç-ary complementary sets based on the concatenation of the sequences in Golay pair or set. It is proved the construction in [3] is a special case of the new construction in this paper. The sequences in the constructed complementary sets can be applied in practical OFDM systems where the number of used subcarriers is not a power of two. It is also showed the code rate of our construction is almost twice of the construction in [3] for some special lengths.
FK506 Binding Protein 8 Peptidylprolyl Isomerase Activity Manages a Late Stage of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Folding and Stability*

Background: The cystic fibrosis transmembrane conductance regulator (CFTR), a chloride channel critical for ionic homeostasis in epithelial cells, is mutated in cystic fibrosis. Results: FKBP8 stabilizes WT and ΔF508 CFTR in the ER and appears to act downstream of Hsp90. Conclusion: FKBP8 is critical for the biogenesis of WT and ΔF508 CFTR. Significance: Our findings suggest that FKBP8 is a late acting chaperone for WT and ΔF508 CFTR. Cystic fibrosis (CF) is caused by mutations in the apical chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) with 90% of patients carrying at least one deletion of the F508 (ΔF508) allele. This mutant form of CFTR is characterized by a folding and trafficking defect that prevents exit from the endoplasmic reticulum. We previously reported that ΔF508 CFTR can be recovered in a complex with Hsp90 and its co-chaperones as an on-pathway folding intermediate, suggesting that Δ508 CF disease arises due to a failure of the proteostasis network (PN), which manages protein folding and degradation in the cell. We have now examined the role of FK506-binding protein 8 (FKBP8), a component of the CFTR interactome, during the biogenesis of wild-type and ΔF508 CFTR. FKBP8 is a member of the peptidylprolyl isomerase family that mediates the cis/trans interconversion of peptidyl prolyl bonds. Our results suggest that FKBP8 is a key PN factor required at a post-Hsp90 step in CFTR biogenesis. In addition, changes in its expression level or alteration of its activity by a peptidylprolyl isomerase inhibitor alter CFTR stability and transport. We propose that CF is caused by the sequential failure of the prevailing PN pathway to stabilize ΔF508-CFTR for endoplasmic reticulum export, a pathway that can be therapeutically managed.
Rate of Conversion from Prodromal Alzheimer's Disease to Alzheimer's Dementia: A Systematic Review of the Literature

Background: The purpose of this study was to summarize published estimates for conversion from mild cognitive impairment or amnestic mild cognitive impairment to Alzheimer's dementia. We carried out a systematic review of English language publications to identify cohort studies published since January 2006 that reported the risk or rate of conversion. Summary: Thirty-two cohort studies were identified, of which 14 reported annualized conversion rates (ACRs). Conversions over 1 year ranged from 10.2 to 33.6% (5 studies, median: 19.0%), and over 2 years from 9.8 to 36.3% (7 studies, median: 18.6%). ACRs ranged from 7.5 to 16.5% (7 studies, median: 11.0%) per person-year for studies recruiting from clinics, and from 5.4 to 11.5% (7 studies, median: 7.1%) for community samples. Key Message: Extensive variation was observed in conversion rates due to the population sampled, diagnostic criteria, and duration, and because many studies did not account for loss to follow-up.
Chinese Poetry Generation with Planning based Neural Network

Chinese poetry generation is a very challenging task in natural language processing. In this paper, we propose a novel two-stage poetry generating method which first plans the sub-topics of the poem according to the user’s writing intent, and then generates each line of the poem sequentially, using a modified recurrent neural network encoder-decoder framework. The proposed planning-based method can ensure that the generated poem is coherent and semantically consistent with the user’s intent. A comprehensive evaluation with human judgments demonstrates that our proposed approach outperforms the state-of-the-art poetry generating methods and the poem quality is somehow comparable to human poets.
PHARMACOKINETICS AND METABOLISM OF A NEW POTENT ANTIEPILEPTIC DRUG, 2,2,3,3-TETRAMETHYCYCLOPROPANECARBONYLUREA, IN RATS

The pharmacokinetics and metabolism of 2,2,3,3-tetramethylcyclopropanecarbonylurea (TMCU), a potent anticonvulsant compound, were studied in male Sprague-Dawley rats following i.v. (5 mg/kg), oral (20 mg/kg), and i.p. (20 mg/kg) administrations. Urine samples were analyzed by gas chromatography-mass spectrometry (GC/MS) and liquid chromatography-mass spectrometry. Plasma samples were analyzed by GC/MS. TMCU absolute bioavailability was 83% and 90% following oral and i.p. dosing, respectively. Following i.p. administration, the peak plasma concentration (Cmax) obtained 45 min after dosing was 15.4 mg/l. Following oral dosing, Cmax was 6.5 mg/l, and it was reached after 4 h. The disposition kinetics of TMCU in rats was adequately described by a one-compartment open body model. TMCU is well distributed into the extravascular tissues with volume of distribution (Vss) of 0.87 l/kg and undergoes extensive metabolism. Only a small fraction of TMCU excreted unmetabolized in the urine (6.3 ± 0.8%). trans-2-Hydroxymethyl-2,3,3-trimethylcyclopropanecarbonylurea (OH-TMCU) was a predominant metabolite of TMCU. Its structure was established by NMR and X-ray crystallography. Following i.p. administration of 5 and 20 mg/kg TMCU, the drug was excreted in the urine as OH-TMCU at an extent of 28.3 ± 2.6% and 42.1 ± 3.8%, respectively. A portion of OH-TMCU was excreted in the urine as TMCU sulfate and TMCU glucuronide.
Optical Performances of Lensless Sub-2micron Pixel for Application in Image Sensors

In this paper we will report on the optical performances of submicron planar lensless pixels arranged in the 2 £ 2 Bayer cell conflguration, the basic element of CMOS colour image sensors. The 2D microlens array placed in front of each pixel in commercial devices has been replaced by a 2D array of submicron holes realised on a thin metal fllm. Each pixel has been designed to present a lightpipe inside its structure acting as an optical waveguide that conflnes the light up to photodiode surface. This pixel design is fully compatible with large scale industry production since its fabrication involves only standard lithographic and etching procedures. Simulations of the light propagation inside the lensless pixel has been performed by using full 3D electromagnetic analysis. In this way it was possible to determine the optical performances of the Bayer cell in terms of the normalized optical e-ciency and crosstalk efiects between adjacent pixels that result to be up to 30% and a factor 10, respectively, better than those ones obtained for the microlens counterpart. The signiflcant increase of the achievable values of the normalized optical e-ciency and crosstalk can foresee the possibility to reduce the pixel size down to 1"m, i.e., beyond the limit imposed by the difiraction efiects arising in microlens equipped pixel.