Miracle-dz/UniFAR-FTUs huggingface dataset:
Two Perturbations for Geometry Optimization of Off‐lattice Bead Protein Models

Referring to the optimization algorithm previously developed for atomic clusters, the present author develops an efficient method for geometry optimization of a coarse‐grained protein model expressed with two kinds of beads (hydrophilic and hydrophobic ones). In the method, two types of geometrical perturbations, center‐directed bead move and one bead rotation, are used to explore new configurations and local optimizations are performed after the perturbations. The center‐directed bead move is used for hydrophobic beads and the one bead rotation is performed for both hydrophobic and hydrophilic beads. The optimization method was applied to protein models consisting of 13, 20, 21, and 34 beads. The present method produced the global minima of the 13‐, 21‐, and 34‐bead models reported in the literature and updated the lowest energies of the protein models with 20 beads. These results indicate that the present method is efficient for searching for optimal structures of proteins.
Evolution of the blood–brain barrier in newly forming multiple sclerosis lesions

Multiple sclerosis (MS) lesions develop around small, inflamed veins. New lesions enhance with gadolinium on magnetic resonance imaging (MRI), reflecting disruption of the blood–brain barrier (BBB). Single time point results from pathology and standard MRI cannot capture the spatiotemporal expansion of lesions. We investigated the development and expansion of new MS lesions, focusing on the dynamics of BBB permeability.
Endocannabinoid Signaling is Critical for Habit Formation

Extended training can induce a shift in behavioral control from goal-directed actions, which are governed by action-outcome contingencies and sensitive to changes in the expected value of the outcome, to habits which are less dependent on action-outcome relations and insensitive to changes in outcome value. Previous studies in rats have shown that interval schedules of reinforcement favor habit formation while ratio schedules favor goal-directed behavior. However, the molecular mechanisms underlying habit formation are not well understood. Endocannabinoids, which can function as retrograde messengers acting through presynaptic CB1 receptors, are highly expressed in the dorsolateral striatum, a key region involved in habit formation. Using a reversible devaluation paradigm, we confirmed that in mice random interval schedules also favor habit formation compared with random ratio schedules. We also found that training with interval schedules resulted in a preference for exploration of a novel lever, whereas training with ratio schedules resulted in less generalization and more exploitation of the reinforced lever. Furthermore, mice carrying either a heterozygous or a homozygous null mutation of the cannabinoid receptor type I (CB1) showed reduced habit formation and enhanced exploitation. The impaired habit formation in CB1 mutant mice cannot be attributed to chronic developmental or behavioral abnormalities because pharmacological blockade of CB1 receptors specifically during training also impairs habit formation. Taken together our data suggest that endocannabinoid signaling is critical for habit formation.
Effects of long‐term heat stress and dietary restriction on the expression of genes of steroidogenic pathway and small heat‐shock proteins in rat testicular tissue

The aim was to investigate the effects of long‐term heat stress and dietary restriction on the expression of certain genes involving in steroidogenic pathway and small heat‐shock proteins (sHSPs) in rat testis. Sprague Dawley rats (n = 24) were equally divided into four groups. Group I and II were kept at an ambient temperature of 22°C, while Groups III and IV were reared at 38°C for 9 weeks. Feed was freely available for Group I and Group III, while Group II and Group IV were fed 60% of the diet consumed by their ad libitum counterparts. At the end of 9 weeks, testicles were collected under euthanasia. Total RNA was isolated from testis tissue samples. Expression profiles of the genes encoding androgen‐binding protein, follicle‐stimulating hormone receptor, androgen receptor, luteinising hormone receptor, steroidogenic acute regulatory protein (StAR), cyclooxygenase‐2 and sHSP genes were assessed at mRNA levels using qPCR. Long‐term heat stress decreased the expression of StAR and HspB10 genes while dietary restriction upregulated StAR gene expression. The results suggested that long‐term heat stress negatively affected the expression of StAR and HspB10 genes and the dietary restriction was able to reverse negative effect of heat stress on the expression of StAR gene in rat testis.
Exploring the Out-of-School Time Program Ecology of Boy Scouts

Youth development programs, such as Boy Scouts of America, and other out-of-school time programs (e.g., sport), may represent important ecological assets in the lives of youth. Participation in such programs has been linked to indicators of positive youth development, including character virtues. Nuanced relationships exist, however, between involvement in specific sets of out-of-school time programs and indicators of positive youth development. The present study examined character virtues of youth (N = 667) who participated in Boy Scouts of America and in other out-of-school time programs (e.g., sport, band/music, or faith-based activities). Scouts participated in an average of two other out-of-school time programs. There was relatively limited variability, however, in the intensity of out-of-school time program participation. Sport was the other out-of-school time program most frequently engaged in by Scouts. In general, character virtues did not vary in relation to participation breadth or intensity. Limitations of the present study and implications for future research are discussed.
Properties of Near-surface Flows around Active Regions from Helioseismic Holography

A variety of local-helioseismic analyses have shown ~50 m/s flows converging on active regions (ARs). We have examined the average properties of both the 75 strongest converging and 75 strongest diverging flows present in Carrington rotation CR1988 within the uppermost 3 Mm of the Sun. The flows, averaged over 5 days, were deduced from calibrated helioseismic holography measurements applied to MDI observations of CR1988. Inflows associated with ARs typically have maximum speed of between 20 and 60 m/s at about 3 heliocentric degrees from their centers and fall to zero by a radius of 7 degrees. Similar converging flows, however, are prevalent in the quiet Sun. Outflows of similar spatial extent, but signficantly larger speeds, are present diverging from sunspots (i.e. the moat flows). Many of the converging flows in ARs appear to simply mark the boundaries of the moats while others converge on plage regions. In general, large ARs containing sunspots contain a complex mixture of both inflows and outflows which, aside from sunspot moats, also appear similar in property to convective components of the quiet Sun.
ADVISU: Interactive Visualization of Anomalies and Dependencies from Massive Scientific Datasets

In this demo, we present ADVISU (Anomaly and Dependency VISUalization), a powerful interactive system for visual analytics from massive datasets. ADVISU efficiently computes different types of dependencies (FDs, CFDs) and detects data anomalies from databases of large size, i.e., up to several thousands of attributes and millions of records. Real-time and scalable computational methods have been implemented in ADVISU to ensure interactivity and the demonstration is intended to show how these methods scale up for realworld massive scientific datasets in astrophysical and oceanographic application domains. ADVISU provides the users informative and interactive graphical interfaces for visualizing data dependencies and anomalies. It enables the analysis to be refined interactively while recomputing the dependencies and anomalies in user selected subspaces with good performance.
Novel anti‐filamin‐A antibody detects a secreted variant of filamin‐A in plasma from patients with breast carcinoma and high‐grade astrocytoma

Identification of tumor‐derived proteins in the circulation may allow for early detection of cancer and evaluation of therapeutic responses. To identify circulating tumor‐derived proteins, mice were immunized with concentrated culture medium conditioned by human breast cancer cells. Antibodies generated by hybridomas were screened against conditioned media from both normal epithelial cells and tumor cells. Antibody selectively reacting with tumor cell–conditioned media was further characterized. This led to the development of a monoclonal antibody (Alper‐p280) that reacts with a newly identified 280‐kDa secreted variant of human filamin‐A. Circulating filamin‐A was detected in patient plasma samples using Alper‐p280 in an ELISA assay. Human plasma samples from 134 patients with brain, breast, or ovarian cancer, 15 patients with active arthritis, and 76 healthy controls were analyzed. Filamin‐A protein levels in human cell lines and tissues were analyzed by western blotting, immunohistochemistry, and electron and confocal microscopy. Circulating filamin‐A was detected in the plasma of 109 of 143 patients with breast cancer and primary brain tumors. Plasma levels of filamin‐A showed 89.5% sensitivity (95% confidence interval [CI] = 0.67% to 0.99%) and 97.8% specificity (95% CI = 0.88% to 0.99%) for glioblastoma at a cut‐off of 21.0 ng/mL. Plasma levels of filamin‐A (>36.0 ng/mL) had 96.7% sensitivity (95% CI = 0.80% to 0.99%) and 67.8% specificity (95% CI = 0.54% to 0.79%) for metastatic breast cancer. Filamin‐A levels were increased in malignant breast or brain tissues, but not in normal control tissues. Filamin‐A localized to lysosomes in MDA.MB. 231 breast cancer cells, but not in normal human mammary epithelial cells, suggesting that filamin‐A may undergo cancer‐specific processing. Plasma filamin‐A appears to be a specific and sensitive marker for patients with high‐grade astrocytoma or metastatic breast cancer. Additional novel cancer biomarkers have been identified and are being developed alongside Alper‐p280 for use in diagnosis of breast carcinoma and high‐grade astrocytoma, and for use in the evaluation of therapeutic responses. (Cancer Sci 2009; 100: 1748–1756)
Diabetes mellitus associated with arsenic exposure in Bangladesh.

The objective of this study was to assess whether arsenic exposure is a risk factor for diabetes mellitus as indicated in a few earlier studies. Arsenic in drinking water is known to occur in western Bangladesh, and in 1996, two of the authors conducted a survey of the prevalence of diabetes mellitus among 163 subjects with keratosis taken as exposed to arsenic and 854 unexposed individuals. Diabetes mellitus was determined by history of symptoms, previously diagnosed diabetes, glucosuria, and blood sugar level after glucose intake. The crude prevalence ratio for diabetes mellitus among keratotic subjects exposed to arsenic was 4.4 (95% confidence interval 2.5-7.7) and increased to 5.2 (95% confidence interval 2.5-10.5) after adjustment for age, sex, and body mass index. On the basis of a few earlier measurements of arsenic concentrations in drinking water by the authorities in Bangladesh and another 20 new ad hoc analyses, approximate time-weighted exposure levels to arsenic in drinking water could be estimated for each subject. Three time-weighted average exposure categories were created, i.e., less than 0.5, 0.5-1.0, and more than 1.0 mg/liter. For the unexposed subjects, the corresponding prevalence ratios were 1.0, 2.6, 3.9, and 8.8, representing a significant trend in risk (p < 0.001). The result corroborates earlier studies and suggests that arsenic exposure is a risk factor for diabetes mellitus.
On the tracking accuracy of beaconing coexistent with event-driven traffic at the DSRC channel

Accurate vehicle tracking is a principal requirement of vehicle safety critical applications. In vehicle-to-vehicle communication, vehicle tracking is achieved by broadcasting beacon containing state information of the sending vehicle in dedicated short range communication (DSRC) channel. Frequent beacon broadcasting can enhance vehicle tracking accuracy, but also lead to channel congestion in high vehicle density. The state-of-the-art beaconing schemes adapt beacon rate to avoid channel congestion. In this paper, we analyze the impacts of event-driven traffic on the tracking accuracy of beaconing schemes. The simulation results show that tracking accuracy degrades with the increase of event-driven traffic load. Based on the results, we conclude that beacon rate should be carefully determined in order to maintain the tracking accuracy with the existence of event-driven traffic load.
Sterile intra-amniotic inflammation in asymptomatic patients with a sonographic short cervix: prevalence and clinical significance

Abstract Objective: To determine the frequency and clinical significance of sterile and microbial-associated intra-amniotic inflammation in asymptomatic patients with a sonographic short cervix. Methods: Amniotic fluid (AF) samples obtained by transabdominal amniocentesis from 231 asymptomatic women with a sonographic short cervix [cervical length (CL) ≤25 mm] were analyzed using cultivation techniques (for aerobic and anaerobic as well as genital mycoplasmas) and broad-range polymerase chain reaction (PCR) coupled with electrospray ionization mass spectrometry (PCR/ESI-MS). The frequency and magnitude of intra-amniotic inflammation [defined as an AF interleukin (IL)-6 concentration ≥2.6 ng/mL], acute histologic placental inflammation, spontaneous preterm delivery (sPTD), and the amniocentesis-to-delivery interval were examined according to the results of AF cultures, PCR/ESI-MS and AF IL-6 concentrations. Results: Ten percent (24/231) of patients with a sonographic short cervix had sterile intra-amniotic inflammation (an elevated AF IL-6 concentration without evidence of microorganisms using cultivation and molecular methods). Sterile intra-amniotic inflammation was significantly more frequent than microbial-associated intra-amniotic inflammation [10.4% (24/231) versus 2.2% (5/231); p < 0.001]. Patients with sterile intra-amniotic inflammation had a significantly higher rate of sPTD <34 weeks of gestation [70.8% (17/24) versus 31.6% (55/174); p < 0.001] and a significantly shorter amniocentesis-to-delivery interval than patients without intra-amniotic inflammation [median 35, (IQR: 10–70) versus median 71, (IQR: 47–98) days, (p < 0.0001)]. Conclusion: Sterile intra-amniotic inflammation is more common than microbial-associated intra-amniotic inflammation in asymptomatic women with a sonographic short cervix, and is associated with increased risk of sPTD (<34 weeks). Further investigation is required to determine the causes of sterile intra-amniotic inflammation and the mechanisms whereby this condition is associated with a short cervix and sPTD.
Delimiting the Origin of a B Chromosome by FISH Mapping, Chromosome Painting and DNA Sequence Analysis in Astyanax paranae (Teleostei, Characiformes)

Supernumerary (B) chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH) is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.
Modelling the Microgrid and Its Parameter Estimations Considering Fading Channels

As the electricity demand continues to grow and renewable energy resources are incorporated into the grid, an effective dynamic state estimation is required for monitoring and grid synchronization. This paper proposes a microgrid state estimation approach considering the unreliable communication channels. Particularly, the renewable microgrid incorporating distributed energy resources, such as solar panels, are represented as a state-space linear model. Then, the wireless sensor network is adopted to sense the microgrid states. For long-distance transmission, we propose an innovative smart grid infrastructure, which is easy to design and offers a reliable two-way communication. In this infrastructure, the modulated signal is transmitted over an unreliable channel, which causes signal distortions. After demodulation and dequantization, the received signal at the energy management system is used the fading Kalman filter algorithm. Using the tunable forgetting factor in the predicted error covariance step, this algorithm aims to minimize the estimation errors so the estimated states reflect the true system states. Simulations results indicate that the developed approach estimates the system states within 0.25 seconds.
Manipulation of the Growth Hormone-Insulin-Like Growth Factor (GH-IGF) Axis: A Treatment Strategy to Reverse the Effects of Early Life Developmental Programming

Evidence from human clinical, epidemiological, and experimental animal models has clearly highlighted a link between the early life environment and an increased risk for a range of cardiometabolic disorders in later life. In particular, altered maternal nutrition, including both undernutrition and overnutrition, spanning exposure windows that cover the period from preconception through to early infancy, clearly highlight an increased risk for a range of disorders in offspring in later life. This process, preferentially termed “developmental programming” as part of the developmental origins of health and disease (DOHaD) framework, leads to phenotypic outcomes in offspring that closely resemble those of individuals with untreated growth hormone (GH) deficiency, including increased adiposity and cardiovascular disorders. As such, the use of GH as a potential intervention strategy to mitigate the effects of developmental malprogramming has received some attention in the DOHaD field. In particular, experimental animal models have shown that early GH treatment in the setting of poor maternal nutrition can partially rescue the programmed phenotype, albeit in a sex-specific manner. Although the mechanisms remain poorly defined, they include changes to endothelial function, an altered inflammasome, changes in adipogenesis and cardiovascular function, neuroendocrine effects, and changes in the epigenetic regulation of gene expression. Similarly, GH treatment to adult offspring, where an adverse metabolic phenotype is already manifest, has shown efficacy in reversing some of the metabolic disorders arising from a poor early life environment. Components of the GH-insulin-like growth factor (IGF)-IGF binding protein (GH-IGF-IGFBP) system, including insulin-like growth factor 1 (IGF-1), have also shown promise in ameliorating programmed metabolic disorders, potentially acting via epigenetic processes including changes in miRNA profiles and altered DNA methylation. However, as with the use of GH in the clinical setting of short stature and GH-deficiency, the benefits of treatment are also, in some cases, associated with potential unwanted side effects that need to be taken into account before effective translation as an intervention modality in the DOHaD context can be undertaken.
Cachexia Stage, Patient-Generated Subjective Global Assessment, Phase Angle, and Handgrip Strength in Patients with Gastrointestinal Cancer

ABSTRACT The aim of this study was to correlate patients with gastrointestinal cancer, classified according to different stages of cancer cachexia (SCC) as proposed by Fearon, with nutritional assessment tools such as PG-SGA, phase angle (PA), and handgrip strength. One hundred one patients with a mean age of 61.8 ± 12.8 yr, with 58.4% being men were included. 32.6% were malnourished according to the body mass index (BMI). A severe or moderate malnutrition had been diagnosed in 63.3% when assessed using the PG-SGA, 60.4% had decreased handgrip strength, and 57.4% had lower grades of PA. Among the patients in the study, 26% did not have cachexia, 11% had precachexia, 56% cachexia, and 8% refractory cachexia. The PG-SGA, PA, and handgrip strength were associated with cachexia (P ≤ 0.001). An increased risk of death was found in patients with cachexia [RR: 9.1; confidence interval (CI) 95%: 0.1–90.2, P = 0.039], refractory cachexia (RR: 69.4, CI 95%: 4.5–1073.8, P = 0.002), and increased serum C-reactive protein (CRP) levels (P < 0.001). In conclusion, most of the patients with digestive system cancer had cachexia or refractory cachexia in the first nutritional assessment. Nutritional risk, as determined by PG-SGA, was correlated with PA and handgrip strength. High CRP levels, cachexia, and refractory cachexia were prognostic factors for cancer patients.