Miracle-dz/UniFAR-FTUs huggingface dataset:
The C4 Model Grass Setaria Is a Short Day Plant with Secondary Long Day Genetic Regulation

The effect of photoperiod (day:night ratio) on flowering time was investigated in the wild species, Setaria viridis, and in a set of recombinant inbred lines (RILs) derived from a cross between foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis). Photoperiods totaled 24 h, with three trials of 8:16, 12:12 and 16:8 light:dark hour regimes for the RIL population, and these plus 10:14 and 14:10 for the experiments with S. viridis alone. The response of S. viridis to light intensity as well as photoperiod was assessed by duplicating photoperiods at two light intensities (300 and 600 μmol.m-2.s-1). In general, day lengths longer than 12 h delayed flowering time, although flowering time was also delayed in shorter day-lengths relative to the 12 h trial, even when daily flux in high intensity conditions exceeded that of the low intensity 12 h trial. Cluster analysis showed that the effect of photoperiod on flowering time differed between sets of RILs, with some being almost photoperiod insensitive and others being delayed with respect to the population as a whole in either short (8 or 12 h light) or long (16 h light) photoperiods. QTL results reveal a similar picture, with several major QTL colocalizing between the 8 and 12 h light trials, but with a partially different set of QTL identified in the 16 h trial. Major candidate genes for these QTL include several members of the PEBP protein family that includes Flowering Locus T (FT) homologs such as OsHd3a, OsRFT1, and ZCN8/12. Thus, Setaria is a short day plant (flowering quickest in short day conditions) whose flowering is delayed by long day lengths in a manner consistent with the responses of most other members of the grass family. However, the QTL results suggest that flowering time under long day conditions uses additional genetic pathways to those used under short day conditions.
Cyst Ventilation Heterogeneity and Alveolar-Airspace Dilation as Early Disease Markers in Lymphangioleiomyomatosis.

RATIONALE Lymphangioleiomyomatosis (LAM) is a rare disease associated with cystic destruction of the pulmonary parenchyma and chronic respiratory failure, and there are trials underway to determine if early intervention can prevent disease progression. An imaging technique that is sensitive to early regional disease would therefore be valuable for patient care and clinical trials. OBJECTIVES We postulated that hyperpolarized 129Xe MRI would be sensitive to ventilation abnormalities and alveolar-airspace dilation in patients with mild LAM disease and normal pulmonary function and that 129Xe MRI would reveal important features of cyst ventilation. METHODS 129Xe ventilation and diffusion-weighted MR images were acquired in 22 LAM patients during two breath-holds of hyperpolarized 129Xe. 129Xe ventilation defect percentage (VDP; percentage of voxels <60% of the mean whole-lung 129Xe MRI signal) and apparent-diffusion coefficient (ADC), a measure of alveolar-airspace size, were quantified and compared to pulmonary-function test (PFT) parameters with Spearman statistics. Sixteen of the LAM patients had a recent, clinical chest CT scan available, and cyst ventilation was assessed by thresholding cysts on the CT images and registration to the 129Xe ventilation images. RESULTS Ventilation deficits were observed in all LAM patients including those with normal pulmonary function and few cysts, and the mean VDP was 19.2% (95% CI 14.8%-23.5%). 129Xe VDP was strongly correlated with FEV1/FVC ratio (r = -0.51, p= 0.02) and DLCO (r = -0.60, p = 0.009), but not with FEV1 (r = -0.33, p = 0.13), likely due to the sensitivity of 129Xe MRI to mild LAM disease in patients with normal FEV1. The mean ADC was 0.048 cm2/s (95% CI 0.042-0.053 cm2/s), and in many cases, ADC was elevated relative values previously reported in adults, and ADC was correlated with the three PFT parameters (p ≤ 0.02). Co-registered 129Xe MRI and CT revealed considerable ventilation heterogeneity within individual LAM patients and across LAM patients with similarly-sized cysts. CONCLUSIONS 129Xe MRI is sensitive to early ventilation abnormalities and airspace dilation in LAM patients with mild disease, and ventilation within the LAM cysts is heterogeneous. 129Xe MRI provides a means to assess the complex regional ventilation and alveolar-airspace size changes of LAM, and the sensitivity of 129Xe MRI to early LAM disease changes is appealing as a future tool for screening and managing patients and for measuring treatment efficacy.
Novel Insights into miRNA Regulation of Storage Protein Biosynthesis during Wheat Caryopsis Development under Drought Stress

Drought stress is a significant abiotic stress factor that affects wheat yield and quality. MicroRNA (miRNA) plays an important role in regulating caryopsis development in response to drought stress. However, little is known about the expression characteristics of miRNAs and how they regulate protein accumulation in wheat caryopsis under drought stress. To address this, two small RNA libraries of wheat caryopsis under control and drought stress conditions were constructed and sequenced. A total of 125 miRNAs were identified in the two samples, of which 110 were known and 15 were novel. A total of 1,981 miRNA target genes were predicted and functional annotations were obtained from various databases for 1,641 of them. Four miRNAs were identified as differential expression under drought stress, and the expression patterns of three of them were consistent with results obtained by reverse transcription polymerase chain reaction (RT-PCR) and reverse transcription quantitative polymerase chain reaction (RT-qPCR). Moreover, three miRNA-target pairs showed negative regulation tendency, as revealed by RT-qPCR. Functional enrichment and pathway analysis revealed that four pathways might be involved in storage protein biosynthesis. Furthermore, drought stress significantly increased the accumulation of protein bodies and protein content in wheat endosperm. In summary, our findings suggest that drought stress may enhance storage protein by regulating the expression of miRNAs and their target genes.
Derivation of Lorentz Invariance and Three Space Dimensions in Generic Field Theory

A very general quantum eld theory, which is not even assumed to be Lorentz invariant, is studied in the limit of very low energy excitations. Fermion and Boson eld theories are considered in parallel. Remarkably, in both cases it is argued that, in the free and lowest energy approximation, a relativistic theory with just three space and one time dimension emerges for each particle type separately. In the case of Fermion elds it is in the form of the Weyl equation, while in the case of the Bosons it is essentially in the form of the Maxwell equations.
How to use virological tools for the optimal management of chronic hepatitis C

Approximately 180 million individuals are chronically infected with hepatitis C, which is strongly associated with the development of cirrhosis, end‐stage liver disease and hepatocellular carcinoma. Several virological tools (anti‐HCV antibody assays, measurement of HCV‐RNA, HCV‐genotyping) are useful in management of hepatitis C infected patients. The primary goal of antiviral therapy in chronic hepatitis C is a sustained virological response (SVR). The HCV genotype should be determined in every patient considered for antiviral therapy because the currently recommended treatment duration and ribavirin doses differ among HCV genotypes. Exact subtyping might gain increased importance for future therapies with direct‐acting antiviral agents (DAA) because of differences of antiviral activities and barriers to resistance among HCV subtypes. Monitoring HCV RNA by a highly sensitive assay (LOD≤15 IU/ml) is the basis for management of response guided therapy of chronic hepatitis C with pegylated IFN plus ribavirin. Rules for early discontinuation of antiviral therapy in non‐responders and determination of optimal treatment durations in virologic responders have been developed for application of individualized treatment strategies.
Nitrogen Front Evolution in Purged Polymer Electrolyte Membrane Fuel Cell with Dead-Ended Anode

In this paper, we model and experimentally verify the evolution of liquid water and nitrogen fronts along the length of the anode channel in a proton exchange membrane fuel cell operating with a dead-ended anode that is fed by dry hydrogen. The accumulation of inert nitrogen and liquid water in the anode causes a voltage drop, which is recoverable by purging the anode. Experiments were designed to clarify the effect of N2 blanketing, water plugging of the channels, and flooding of the gas diffusion layer. The observation of each phenomenon is facilitated by simultaneous gas chromatography measurements on samples extracted from the anode channel to measure the nitrogen content and neutron imaging to measure the liquid water distribution. A model of the accumulation is presented, which describes the dynamic evolution of a N2 blanketing front in the anode channel leading to the development of a hydrogen starved region. The prediction of the voltage drop between purge cycles during nonwater plugging channel conditions is shown. The model is capable of describing both the two-sloped behavior of the voltage decay and the time at which the steeper slope begins by capturing the effect of H2 concentration loss and the area of the H2 starved region along the anode channel.
OPCML Is a Broad Tumor Suppressor for Multiple Carcinomas and Lymphomas with Frequently Epigenetic Inactivation

Background Identification of tumor suppressor genes (TSGs) silenced by CpG methylation uncovers the molecular mechanism of tumorigenesis and potential tumor biomarkers. Loss of heterozygosity at 11q25 is common in multiple tumors including nasopharyngeal carcinoma (NPC). OPCML, located at 11q25, is one of the downregulated genes we identified through digital expression subtraction. Methodology/Principal Findings Semi-quantitative RT-PCR showed frequent OPCML silencing in NPC and other common tumors, with no homozygous deletion detected by multiplex differential DNA-PCR. Instead, promoter methylation of OPCML was frequently detected in multiple carcinoma cell lines (nasopharyngeal, esophageal, lung, gastric, colon, liver, breast, cervix, prostate), lymphoma cell lines (non-Hodgkin and Hodgkin lymphoma, nasal NK/T-cell lymphoma) and primary tumors, but not in any non-tumor cell line and seldom weakly methylated in normal epithelial tissues. Pharmacological and genetic demethylation restored OPCML expression, indicating a direct epigenetic silencing. We further found that OPCML is stress-responsive, but this response is epigenetically impaired when its promoter becomes methylated. Ecotopic expression of OPCML led to significant inhibition of both anchorage-dependent and -independent growth of carcinoma cells with endogenous silencing. Conclusions/Significance Thus, through functional epigenetics, we identified OPCML as a broad tumor suppressor, which is frequently inactivated by methylation in multiple malignancies.
A 1-V 416-nW fully integrated sensor interface IC for pacemakers

An ultra-low-power, low-noise sensor interface IC for pacemakers is presented. The proposed architecture is designed to achieve small chip area and a good trade-off between power consumption and noise figure by using current-mode operation. The IECG signal, from 50mHz-100Hz, is first filtered by a bandpass filter. Subsequently, the signal output of the filter is converted into a current by a nonlinear transconductance (Gm) cell. The output of the Gm-cell is digitized by a nonlinear 8-bit 1kS/s Current-mode Successive Approximation ADC to compensate for the nonlinearity of the Gm-cell. The simulated input-referred noise is 5. 48μVrms, achieving a Noise Efficiency Factor of 3.3, and the simulated power consumption for the overall system is 416 nW while operating from a 1 V supply.
Accelerating SNARE-Mediated Membrane Fusion by DNA-Lipid Tethers.

SNARE proteins are the core machinery to drive fusion of a vesicle with its target membrane. Inspired by the tethering proteins that bridge the membranes and thus prepare SNAREs for docking and fusion, we developed a lipid-conjugated ssDNA mimic that is capable of regulating SNARE function, in situ. The DNA-lipid tethers consist of a 21 base pairs binding segment at the membrane distal end that can bridge two liposomes via specific base-pair hybridization. A linker at the membrane proximal end is used to control the separation distance between the liposomes. In the presence of these artificial tethers, SNARE-mediated lipid mixing is significantly accelerated, and the maximum fusion rate is obtained with the linker shorter than 40 nucleotides. As a programmable tool orthogonal to any native proteins, the DNA-lipid tethers can be further applied to regulate other biological processes where capturing and bridging of two membranes are the prerequisites for the subsequent protein function.
The microtubule binding domain of microtubule-associated protein MAP1B contains a repeated sequence motif unrelated to that of MAP2 and tau

We report the complete sequence of the microtubule-associated protein MAP1B, deduced from a series of overlapping genomic and cDNA clones. The encoded protein has a predicted molecular mass of 255,534 D and contains two unusual sequences. The first is a highly basic region that includes multiple copies of a short motif of the form KKEE or KKEVI that are repeated, but not at exact intervals. The second is a set of 12 imperfect repeats, each of 15 amino acids and each spaced by two amino acids. Subcloned fragments spanning these two distinctive regions were expressed as labeled polypeptides by translation in a cell-free system in vitro. These polypeptides were tested for their ability to copurify with unlabeled brain microtubules through successive cycles of polymerization and depolymerization. The peptide corresponding to the region containing the KKEE and KKEVI motifs cycled with brain microtubules, whereas the peptide corresponding to the set of 12 imperfect repeats did not. To define the microtubule binding domain in vivo, full-length and deletion constructs encoding MAP1B were assembled and introduced into cultured cells by transfection. The expression of transfected polypeptides was monitored by indirect immunofluorescence using anti-MAP1B-specific antisera. These experiments showed that the basic region containing the KKEE and KKEVI motifs is responsible for the interaction between MAP1B and microtubules in vivo. This region bears no sequence relationship to the microtubule binding domains of kinesin, MAP2, or tau.
Varying Constants, Gravitation and Cosmology

Fundamental constants are a cornerstone of our physical laws. Any constant varying in space and/or time would reflect the existence of an almost massless field that couples to matter. This will induce a violation of the universality of free fall. Thus, it is of utmost importance for our understanding of gravity and of the domain of validity of general relativity to test for their constancy. We detail the relations between the constants, the tests of the local position invariance and of the universality of free fall. We then review the main experimental and observational constraints that have been obtained from atomic clocks, the Oklo phenomenon, solar system observations, meteorite dating, quasar absorption spectra, stellar physics, pulsar timing, the cosmic microwave background and big bang nucleosynthesis. At each step we describe the basics of each system, its dependence with respect to the constants, the known systematic effects and the most recent constraints that have been obtained. We then describe the main theoretical frameworks in which the low-energy constants may actually be varying and we focus on the unification mechanisms and the relations between the variation of different constants. To finish, we discuss the more speculative possibility of understanding their numerical values and the apparent fine-tuning that they confront us with.
CME ACTIVITY: Microbial Interactions during Upper Respiratory Tract Infections

Moraxella catarrhalis, and Staphylococcus aureus often colonize the nasopharynx. Children are susceptible to bacterial infections during or soon after upper respiratory tract infection (URI). We describe colonization with these 4 bacteria species alone or in combination during URI. Data were from a prospective cohort of healthy children 6 to 36 months of age followed up for 1 year. Analyses of 968 swabs from 212 children indicated that S. pneumoniae colonization is negatively associated with colonization by H. infl uenzae. Competitive interactions shifted when H. infl uenzae and M. catarrhalis colonized together. In this situation, the likelihood of colonization with all 3 species is higher. Negative associations were identifi ed between S. pneumoniae and S. aureus and between H. infl uenzae and S. aureus. Polymicrobial interactions differed by number and species of bacteria present. Antimicrobial therapy and vaccination strategies targeting specifi c bacterial species may alter the fl ora in unforeseen ways. S pneumoniae, Haemophilus infl uenzae, Moraxella catarrhalis, and Staphylococcus aureus often asymptomatically colonize the nasopharynx of young children and are also associated with disease. S. pneumoniae, H. infl uenzae, and M. catarrhalis are the 3 most common otitis media pathogens (1,2). S. pneumoniae are also common causes of pneumonia, sepsis, and meningitis in young children (3). The proportion of young children colonized with any of these 3 bacteria species can be >50% in certain populations (4–6). S. aureus strains colonize up to 35% of young children and are associated with a wide range of diseases including soft tissue infections, sepsis, and pneumonia (7,8). Increases in the incidence of disease caused by community-acquired methicillin-resistant S. aureus are of great concern (9). Host factors have been shown to in? uence colonization with S. pneumoniae, H. infl uenzae, M. catarrhalis, and S. aureus. These include host immunity, age, gender, race, out-of-home daycare, breastfeeding, and environmental exposure to tobacco smoke (10). The magnitude of host effects may differ by bacteria species. Interactions between bacteria in? uence which species persist in the nasopharynx (11–13). Bacteria species may Microbial Interactions during Upper Respiratory Tract Infections
Investigation of the Relationship Between Retinol Binding Protein 4, Metabolic Syndrome and Insulin Resistance in Iranian Obese 5-17 Year Old Children

Objective Retinol-binding protein 4 (RBP4) has recently been reported to be associated with insulin resistance (IR) and the metabolic syndrome by a number of researchers in various populations. However, controversies are present among different studies, which might be due to the differences between various ethnic, age, and sex groups. This study aimed to determine whether RBP4 can be assumed as a marker of IR and the metabolic syndrome in the Iranian obese children. Methods In the present longitudinal cross-sectional study, 100 5-17 years old obese children were recruited from January 1, 2011 to February 1, 2012. The patients’ information including the demographic variables, health status and behavior, and daily physical activity were collected. Moreover, serum RBP4 was measured and correlated with the homeostasis model assessment of IR index (HOMA-IR), components of the metabolic syndrome, and lipoprotein metabolism. Findings The results revealed a positively significant correlation between RBP4 and the HOMA-IR index (P=0.02). Partial Spearman test also revealed a significant correlation between RBP4 plasma concentrations and the components of the metabolic syndrome, including waist circumference, systolic (but not diastolic) blood-pressure, and fasting blood sugar (P<0.05). However, no significant correlation was observed between RBP4 and HDL (P=0.3) as well as triglycerides concentration (P=0.1). Moreover, plasma RBP4 level gradually increased with the increasing number of the metabolic syndrome components. Conclusion Regarding the results of the present study and previous investigations, RBP4 seems to be a suggestible predictive marker for both insulin resistance and metabolic syndrome in Iranian obese children; however, further studies are needed to be conducted among different ethnicities and age groups in order to determine the predictive value of this correlation.
Control on landscapes with local minima and flat regions: A simulated annealing and gain scheduling approach

Landscapes containing local minima and ¿flat¿ regions are frequently encountered in multi-layer neural networks that employ sigmoid-like activation function in the hidden layers. Numerous techniques in the neural network community have been proposed to address these issues. In this note, we extend these ideas to the neural network control of nonlinear systems. We propose a solution which employs simulated annealing and a gain scheduled learning rate.
Multicenter independent assessment of outcomes in chronic myeloid leukemia patients treated with imatinib.

BACKGROUND Imatinib slows development of chronic myeloid leukemia (CML). However, available information on morbidity and mortality is largely based on sponsored trials, whereas independent long-term field studies are lacking. PATIENTS AND METHODS Consecutive CML patients who started imatinib treatment before 2005 and who were in complete cytogenetic remission (CCyR) after 2 years (± 3 months) were eligible for enrollment in the independent multicenter Imatinib Long-Term (Side) Effects (ILTE) study. Incidence of the first serious and nonserious adverse events and loss of CCyR were estimated according to the Kaplan-Meier method and compared with the standard log-rank test. Attainment of negative Philadelphia chromosome hematopoiesis was assessed with cytogenetics and quantitative polymerase chain reaction. Cumulative incidence of death related or unrelated to CML progression was estimated, accounting for competing risks, according to the Kalbleisch-Prentice method. Standardized incidence ratios were calculated based on population rates specific for sex and age classes. Confidence intervals were calculated by the exact method based on the χ(2) distribution. All statistical tests were two-sided. RESULTS A total of 832 patients who were treated for a median of 5.8 years were enrolled. There were 139 recorded serious adverse events, of which 19.4% were imatinib-related. A total of 830 nonserious adverse events were observed in 53% of patients; 560 (68%) were imatinib-related. The most frequent were muscle cramps, asthenia, edema, skin fragility, diarrhea, tendon, or ligament lesions. Nineteen patients (2.3%) discontinued imatinib because of drug-related toxic effects. Forty-five patients lost CCyR, at a rate of 1.4 per 100 person-years. Durable (>1 year) negative Philadelphia chromosome hematopoiesis was attained by 179 patients. Twenty deaths were observed, with a 4.8% mortality incidence rate (standardized incidence ratio = 0.7; 95% confidence interval = 0.40 to 1.10, P = .08), with only six (30%) associated with CML progression. CONCLUSIONS In this study, CML-related deaths were uncommon in CML patients who were in CCyR 2 years after starting imatinib, and survival was not statistically significantly different from that of the general population.