Miracle-dz/UniFAR-FTUs huggingface dataset:
Rare recombination events generate sequence diversity among balancer chromosomes in Drosophila melanogaster

Significance Balancer chromosomes are highly rearranged chromosomes that suppress recombination and are an important tool in Drosophila genetics, yet their precise molecular structure is unknown. Here we characterize the inversion breakpoints of the X chromosome balancer FM7, and provide evidence that rare double-crossover events with balanced homologs can occur. These rare exchange events do not undermine the use of balancers, but lead to diversity among balancers. We also provide genomic evidence that unequal exchange between duplicated regions underlies reversion at the Bar locus. Our work demonstrates the power of genome sequencing to understand the molecular nature of classical genetic resources, and cautions that mutations maintained over balancers in regions susceptible to exchange should be checked regularly to prevent their loss. Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the Drosophila melanogaster genetic toolkit. Despite their widespread use, the organization of balancer chromosomes has not been characterized at the molecular level, and the degree of sequence variation among copies of balancer chromosomes is unknown. To map inversion breakpoints and study potential diversity in descendants of a structurally identical balancer chromosome, we sequenced a panel of laboratory stocks containing the most widely used X chromosome balancer, First Multiple 7 (FM7). We mapped the locations of FM7 breakpoints to precise euchromatic coordinates and identified the flanking sequence of breakpoints in heterochromatic regions. Analysis of SNP variation revealed megabase-scale blocks of sequence divergence among currently used FM7 stocks. We present evidence that this divergence arose through rare double-crossover events that replaced a female-sterile allele of the singed gene (snX2) on FM7c with a sequence from balanced chromosomes. We propose that although double-crossover events are rare in individual crosses, many FM7c chromosomes in the Bloomington Drosophila Stock Center have lost snX2 by this mechanism on a historical timescale. Finally, we characterize the original allele of the Bar gene (B1) that is carried on FM7, and validate the hypothesis that the origin and subsequent reversion of the B1 duplication are mediated by unequal exchange. Our results reject a simple nonrecombining, clonal mode for the laboratory evolution of balancer chromosomes and have implications for how balancer chromosomes should be used in the design and interpretation of genetic experiments in Drosophila.
Bromocriptine: A Sympatholytic, D2-Dopamine Agonist for the Treatment of Type 2 Diabetes

Bromocriptine is a sympatholytic D2-dopamine agonist that has been approved for the treatment of type 2 diabetes. Based on animal and human studies, timed bromocriptine administration within 2 h of awakening is believed to augment low hypothalamic dopamine levels and inhibit excessive sympathetic tone within the central nervous system (CNS), resulting in a reduction in postmeal plasma glucose levels due to enhanced suppression of hepatic glucose production. Bromocriptine has not been shown to augment insulin secretion or enhance insulin sensitivity in peripheral tissues (muscle). Addition of bromocriptine to poorly controlled type 2 diabetic patients treated with diet alone, metformin, sulfonylureas, or thiazolidinediones produces a 0.5–0.7 decrement in HbA1c. Bromocriptine also reduces fasting and postmeal plasma free fatty acid (FFA) and triglyceride levels. In a 52 double-blind, placebo-controlled study in type 2 diabetic patients, bromocriptine reduced the composite cardiovascular end point by 40%. The mechanism of the drug’s beneficial effect on cardiovascular disease remains to be determined. ### Introduction Type 2 diabetes is a chronic metabolic disorder characterized by insulin resistance, impaired β-cell function, and multiple other metabolic/endocrine abnormalities (1). Because of its multifactorial pathogenesis, restoration of normoglycemia is difficult to achieve and requires multiple antidiabetic medications that have different mechanisms of action and can be used in combination to produce an additive effect (1,2). Therefore, the development of antidiabetic agents that have novel mechanisms of action and can be used in combination with currently approved medications for the treatment of type 2 diabetes is highly desirable. Type 2 diabetic patients are at high risk for atherosclerotic cardiovascular complications (3). Although hyperglycemia is a risk factor for coronary artery disease and stroke, it is a relatively weak risk factor compared with other more established risk factors such as dyslipidemia, hypertension, obesity, and the insulin resistance (metabolic) syndrome (4, …
Biodegradation and Mechanical Properties of Poly(lactic acid)/Poly(butylene succinate) Blends

Polymer blends were fabricated with poly(lactic acid) (PLA) with better mechanical properties and poly(butylene succinate) (PBSU) with better biodegradable properties to clarify the effect of the blending ratio on the biodegradable and mechanical properties of the blends. The specimens were heat treated to improve the reduction in stiffness due to blending. Hydrolysis and soil burial tests up to 16 weeks were conducted to investigate the biodegradation properties. Young's modulus increased with increasing contents of PLA, whereas tensile strength is lowest in the PLA/PBSU (50/50) polymer blend before biodegradation because of the immiscibility of PLA and PBSU. Young's modulus kept constant up 16 weeks both in the hydrolysis and the soil burial tests. On the other hand, tensile strength decreased remarkably in the hydrolysis tests. The observation results of the specimen surface and the fracture surface indicate that the surface and bulk degradation occur in hydrolysis and soil burial tests, respectively
Noncommutative U(1) instantons in eight dimensional Yang-Mills theory

We study the noncommutative version of the extended ADHM construction in the eight dimensional U(1) Yang-Mills theory. This construction gives rise to the solutions of the BPS equations in the Yang-Mills theory, and these solutions preserve at least 3/16 of supersymmetries. In a wide subspace of the extended ADHM data, we show that the integer $k$ which appears in the extended ADHM construction should be interpreted as the $D4$-brane charge rather than the $D0$-brane charge by explicitly calculating the topological charges in the case that the noncommutativity parameter is anti-self-dual. We also find the relationship with the solution generating technique and show that the integer $k$ can be interpreted as the charge of the $D0$-brane bound to the $D8$-brane with the $B$-field in the case that the noncommutativity parameter is self-dual.
A simplified model for gasification of oil palm empty fruit bunch briquettes

This study is aimed at investigating the product gas yield and composition of EFB briquettes gasification using a simplified stoichiometric equilibrium model. Similar mathematical models have been successfully adopted by a number of research groups to investigate the thermochemical conversion of biomass species. Hence the effect of gasification temperature on the product gas yield and composition of EFB briquettes gasification using a simplified stoichiometric equilibrium model is presented in this study. The results indicate that the H2 and CO content increased with increasing temperature from 600 to 800°C while the CO2, N2 and CH4 content decreased. The H2 content increased with increasing temperature, with peak production of 25.55 mol % at 750°C. The HHV (4.87 to 8.38 MJ/Nm3), CGE (27.72 to 47.71%) and CCE (25.42 to 41.54%) values increased with increasing temperature during gasification. Hence for a reacting system with known reaction mechanism, the model can be used to reasonably deduce the yield and composition of the gasification products.
Low- and High-Ionization Absorption Properties of Mg II Absorption-selected Galaxies at Intermediate Redshifts. I. General Properties

We present extensive metal-line absorption properties for 45 absorption systems that were selected by their Mg II absorption at redshifts between 0.4 and 1.4. For each system the properties of several chemical species are determined, including a wide range of ionization conditions. In the optical, the absorption systems have been observed at ∼6 km s-1 resolution with HIRES/Keck, which covered Mg II, several Fe II transitions, Mg I, and in some cases (depending upon redshift) Ca II, Ti II, Mn II, and Al III. Ultraviolet, lower resolution (∼230 km s-1) Faint Object Spectrograph data (1600-3275 Å) were obtained from the Hubble Space Telescope archive. These spectra covered Al II, Al III, Si II, Si III, Si IV, C II, C III, C IV, N V, O VI, and several Lyman series transitions, with coverage dependent upon the absorption system redshift. From these data, we infer that Mg II-absorbing galaxies at intermediate redshifts have multiphase gaseous structures.
MetastamiRs: Non-Coding MicroRNAs Driving Cancer Invasion and Metastasis

MicroRNAs (miRNAs) are small non-coding RNAs of ~22 nucleotides that function as negative regulators of gene expression by either inhibiting translation or inducing deadenylation-dependent degradation of target transcripts. Notably, deregulation of miRNAs expression is associated with the initiation and progression of human cancers where they act as oncogenes or tumor suppressors contributing to tumorigenesis. Abnormal miRNA expression may provide potential diagnostic and prognostic tumor biomarkers and new therapeutic targets in cancer. Recently, several miRNAs have been shown to initiate invasion and metastasis by targeting multiple proteins that are major players in these cellular events, thus they have been denominated as metastamiRs. Here, we present a review of the current knowledge of miRNAs in cancer with a special focus on metastamiRs. In addition we discuss their potential use as novel specific markers for cancer progression.
Molecular Machinery Regulating Exocytosis

Exocytosis is the major intracellular route for the delivery of proteins and lipids to the plasma membrane and the means by which vesicular contents are released into the extracellular space. The anterograde trafficking of vesicles to the plasma membrane is vital for membrane expansion during cell division; cell growth and migration; the delivery of specialised molecules to establish cell polarity; cell-to-cell communication; neurotransmission and the secretion of response factors such as hormones, cytokines and antimicrobial peptides. There are two major trafficking routes in eukaryotic cells, which are referred to as constitutive and regulated (Ory & Gasman, 2011). Constitutive exocytosis involves the steady state delivery of secretory carrier vesicles from the endoplasmic reticulum via the Golgi apparatus to the plasma membrane (Lacy & Stow, 2011). Regulated or granule-mediated exocytosis involves a specific trigger, usually a burst of intracellular calcium following an extrinsic stimulus. This system is utilized for secretion in neuronal cells and other specialist secretory cells, such as neuroendocrine, endocrine and exocrine cells (Burgoyne & Morgan, 2003; Jolly & Sattentau, 2007; Lacy & Stow, 2011). Regulated exocytosis enables a rapid response from a subpopulation of vesicles already primed and competent for fusion (Manjithaya & Subramani, 2011; Nickel & Seedorf, 2008; Nickel, 2010). Regulated exocytosis is also used for polarised traffic of vesicular membrane and cargo to specific spatial landmarks and this is particularly important during times of dramatic change in cell morphology, such as cell division, cell motility, phagocytosis and axonal outgrowth.
Effect of oat intake on glycaemic control and insulin sensitivity: a meta-analysis of randomised controlled trials

The present meta-analysis of randomised controlled trials (RCT) aimed to investigate the effect of oat intake on glycaemic control and insulin sensitivity. A literature search was carried out in PubMed, ScienceDirect Online and The Cochrane Library (up to October 2013) for RCT that assessed the effect of oat intake on glucose control and insulin sensitivity. A total of fifteen articles with 673 subjects met the inclusion criteria. A random-effects model was used when the overall pooled studies exhibited significant heterogeneity. Otherwise, a fixed-effects model was used. Compared with controls, oat intake significantly reduced the concentrations of fasting insulin by − 6·29 (95 % CI − 12·32, − 0·27) pmol/l (P= 0·04) and the values of glucose AUC (GAUC; 0–120 min) by − 30·23 (95 % CI − 43·65, − 16·81) min × mmol/l (P< 0·0001). There was a slight decrease in fasting glucose concentrations, glycated Hb concentrations and homeostatic model assessment-insulin resistance values in subjects who consumed oats, but the difference was not significant. In conclusion, oat intake significantly lowers fasting insulin concentrations and GAUC values. To further investigate the effect of oat intake on fasting glucose concentrations, additional long-term and high-quality RCT with a parallel design are required.
Calcium‐induced calcium release in rat sensory neurons.

1. In isolated dorsal root ganglion cells (DRG neurons), changes in the concentration of global cytosolic Ca2+ (delta [Ca2+]c) were measured by the fluorescence of K5‐indo‐1. Depolarizations from ‐60 to 0 mV (500 ms) and Ca2+ influx through Ca2+ channels (ICa) increased [Ca2+]c by 480 +/‐ 113 nM, the peak occurring 542 +/‐ 76 ms (mean +/‐ S.E.M.) after repolarization. 2. Ryanodine (10 microM) reduced depolarization‐induced delta [Ca2+]c by up to 80% and blocked delta [Ca2+]c induced by 20 mM caffeine. 3. Peak delta [Ca2+]c and peak ICa followed a similar bell‐shaped voltage dependence. Removal of extracellular Ca2+ abolished depolarization‐induced delta [Ca2+]c; its elevation from 2 to 8 mM increased peak ICa by 30% and delta [Ca2+]c by 108%. 4. Ca2+ influx at 0 mV was graded by pulse durations between 20 and 500 ms. Up to 200 ms, delta [Ca2+]c increased linearly with Ca2+ influx. Depolarizations longer than 200 ms induced a supralinear increase in delta [Ca2+]c that was abolished by caffeine (20 mM). 5. The supralinear increase in delta [Ca2+]c and the caffeine‐induced delta [Ca2+]c were measured only in thirteen of nineteen DRG neurons; in the other six of nineteen cells both properties were absent. The results suggest that Ca(2+)‐induced Ca2+ release (CICR) is expressed differently in different populations of DRG neurons. 6. A single action potential did not significantly increase [Ca2+]c. Trains of stimuli (20 Hz) induced delta [Ca2+]c that linearly increased with the number of action potentials. Delta [Ca2+]c due to 100 action potentials had a significant ryanodine‐sensitive component. 7. It is discussed that CICR can contribute to the depolarization‐induced [Ca2+]c, provided the Ca2+ influx lasts for a certain minimum period of time.
Numerical simulation of the coupled turbulent flow and macroscopic solidification in continuous casting with Electromagnetic Brake

A computer program has been developed for analyzing the three-dimensional, steady conservation equations for transport phenomena in a slab continuous casting process with Electromagnetic Brake (EMBr) to investigate the effect of EMBr on the turbulent melt-flow, temperature fields, and macroscopic solidification of the molten metal. The enthalpy-porosity relation was employed to suppress the velocity within a mushy region. A revised low-Reynolds number k-e turbulence model was used to consider the turbulent effects. The electromagnetic field was described by Maxwell equations. The application of EMBr to the mold region results in the decrease of the transfer of superheat to the narrow face, the increase of temperature in free-surface region and most part of the melt of submold region, and the higher temperature gradients near the solidifying shell. The increasing magnetic flux density has effect mainly on the surface temperature of the solidifying shell at the narrow face, hardly on that at the wide face. It is seen that in the presence of EMBr, a thicker solidifying shell is obtained at the narrow face of slab.
Star formation bursts in isolated spiral galaxies

We study the response of the gaseous component of a galactic disc to the time-dependent potential generated by N-body simulations of a spiral galaxy. The results show significant variation of the spiral structure of the gas which might be expected to result in significant fluctuations in the star formation rate (SFR). Pronounced local variations of the SFR are anticipated in all cases. Bursty histories for the global SFR, however, require that the mean surface density is much less (around an order of magnitude less) than the putative threshold for star formation. We thus suggest that bursty star formation histories, normally attributed to mergers and/or tidal interactions, may be a normal pattern for gas-poor isolated spiral galaxies.
Prostate cancer screening trends of New York State men at least 50 years of age, 1994 to 1997.

BACKGROUND Despite the lack of consensus on prostate cancer screening recommendations, men are being screened at high rates in some states. Our objective was to examine the trends in prostate cancer screening awareness and practices from 1994 through 1997 and the relationship among screening practices and demographic characteristics, perceived risk, and family history of prostate cancer. METHODS Data from the New York State Behavioral Risk Factor Surveillance System surveys and questionnaire modules on prostate cancer screening were used for this study, which excluded men younger than 50 years of age and men with a history of prostate cancer. The questionnaires were administered by random-digit-dialed monthly telephone surveys of the civilian, noninstitutionalized adult population in New York State. RESULTS A total of 295, 336, 273, and 448 men, the vast majority of whom were white, met the study criteria for 1994, 1995, 1996, and 1997, respectively. Each year the percentage of men who reported having heard of the prostate specific antigen (PSA) test increased (test for trend, P < 0.001). Among those who had heard of the PSA test, the percentage who reported having had a PSA test increased steadily from 1994 to 1997. About 30% of the men in each year's study did not have an impression of their risk of getting prostate cancer. CONCLUSIONS Given the increasing rate at which men are reporting being screened for prostate cancer and given their reported perceived risk levels, perhaps more needs to be done to educate men about screening implications and personal risk for prostate cancer.
Dioscin Inhibits HSC-T6 Cell Migration via Adjusting SDC-4 Expression: Insights from iTRAQ-Based Quantitative Proteomics

Hepatic stellate cells (HSCs) migration, an important bioprocess, contributes to the development of liver fibrosis. Our previous studies have found the potent activity of dioscin against liver fibrosis by inhibiting HSCs proliferation, triggering the senescence and inducing apoptosis of activated HSCs, but the molecular mechanisms associated with cell migration were not clarified. In this work, iTRAQ (isobaric tags for relative and absolution quantitation)-based quantitative proteomics study was carried out, and a total of 1566 differentially expressed proteins with fold change ≥2.0 and p < 0.05 were identified in HSC-T6 cells treated by dioscin (5.0 μg/mL). Based on Gene Ontology classification, String and KEGG pathway assays, the effects of dioscin to inhibit cell migration via regulating SDC-4 were carried out. The results of wound-healing, cell migration and western blotting assays indicated that dioscin significantly inhibit HSC-T6 cell migration through SDC-4-dependent signal pathway by affecting the expression levels of Fn, PKCα, Src, FAK, and ERK1/2. Specific SDC-4 knockdown by shRNA also blocked HSC-T6 cell migration, and dioscin slightly enhanced the inhibiting effect. Taken together, the present work showed that SDC-4 played a crucial role on HSC-T6 cell adhesion and migration of dioscin against liver fibrosis, which may be one potent therapeutic target for fibrotic diseases.
Scientific data management in the coming decade

Scientific instruments and computer simulations are creating vast data stores that require new scientific methods to analyze and organize the data. Data volumes are approximately doubling each year. Since these new instruments have extraordinary precision, the data quality is also rapidly improving. Analyzing this data to find the subtle effects missed by previous studies requires algorithms that can simultaneously deal with huge datasets and that can find very subtle effects --- finding both needles in the haystack and finding very small haystacks that were undetected in previous measurements.
Automatic recognition of physiological parameters in the human voice: Heart rate and skin conductance

We show that high pulse/low pulse, heart rate and skin conductance recognition can reach good accuracies using classification on a large group of 4k audio features extracted from sustained vowels and breathing periods. A database containing audio, heart rate and skin conductance recordings from 19 subjects is established for evaluation of audio-based bio-signal recognition. On this database in speaker-dependent testing, heart rate and skin conductance can be determined with a correlation coefficient of . 861/. 960 and mean absolute error of 8.1 BPM/88.2 μMhO for regression based on sustained vowels recorded from a room microphone. Using the same set-up, a high pulse/low pulse classification can reach an unweighted accuracy of 82.7%. The results are largely independent from microphone type and the two bio-signals can be determined from breathing periods as well. Performance does, however, degrade in speaker-independent setting.
Modeling Dielectric Absorption in Capacitors

Version 2d, June 2008 It is well known that dielectric absorption plays a critical role in determining the accuracy of analog sampled-data systems that are based on charge storage, such as sampleand-holds and switched-capacitor ADCs. Less appreciated, but no less important, is the role it plays in determining the quality factor, or Q, of the capacitor. Dielectric absorption has both storage and loss components that act, and are significant, over the entire usable frequency range of the capacitor.
Pharmacogenomics in osteoporosis: Steps toward personalized medicine

Osteoporosis is a complicated and preventable disease with major morbidity complications that affects millions of people. In the last 15 years, there have been numerous studies and research in the new fields of pharmacogenetics and pharmacogenomics related to osteoporosis. Numerous “candidate genes” have been identified and have been found to be associated with osteoporosis as well as the treatment of osteoporosis. Many studies have found conflicting results on different polymorphisms and whether or not they are related to bone mineral density and osteoporosis. There is a need for larger and better designed pharmacogenomic studies related to osteoporosis incorporating a greater variety of candidate genes. The evaluation of osteoporosis and fracture risk is moving from a risk stratification approach to a more individualized approach, in which an individual’s absolute risk of fracture is evaluable as a constellation of the individual’s environmental exposure and genetic makeup. Therefore, the identification of gene variants associated with osteoporosis phenotypes or response to therapy might help individualize the prognosis, treatment, and prevention of fracture. This review focuses on major candidate genes and what needs to be done to take the genetics of osteoporosis and incorporate them into the pharmacogenomics of the management of osteoporosis.