Miracle-dz/UniFAR-FTUs huggingface dataset:
Accurate description of van der Waals complexes by density functional theory including empirical corrections

An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT‐D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R−6. The use of pure, gradient‐corrected density functionals (BLYP and PBE), together with the resolution‐of‐the‐identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The “double counting” of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene · H2O and four H‐bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT‐D‐BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT‐D data may either be used to calibrate much simpler (e.g., force‐field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1463–1473, 2004
Approximate String Matching for Searching DNA Sequences

—This paper presents a new algorithm for searching short fragments of sequences in long DNA sequences. A short sequence (pattern) is searched in both DNA strands with a given maximal value of errors. Each DNA sequence (T) is preprocessed by compressing it using Burrows-Wheeler transform and wavelet tree. First, the pattern is divided into short words which overlap themselves, and then their positions in T are determined using FM-index. Connections between the words are searched under the assumption of an acceptable maximal error allowed. Experimental results indicate that the algorithm is highly effective and it outperforms a popular Basic Local Alignment Search Tool (BLAST) in case of searching for short sequences.
Improving requirements glossary construction via clustering: approach and industrial case studies

Context. A glossary is an important part of any software requirements document. By making explicit the technical terms in a domain and providing definitions for them, a glossary serves as a helpful tool for mitigating ambiguities. Goal. A necessary step for building a glossary is to decide upon the glossary terms and to identify their related terms. Doing so manually is a laborious task. Our objective is to provide automated support for identifying candidate glossary terms and their related terms. Our work differs from existing work on term extraction mainly in that, instead of providing a flat list of candidate terms, our approach clusters the terms by relevance. Method. We use case study research as the basis for our empirical investigation. Results. We present an automated approach for identifying and clustering candidate glossary terms. We evaluate the approach through two industrial case studies; one study concerns a satellite software component, and the other -- an evidence management tool for safety certification. Conclusions. Our results indicate that over requirements documents: (1) our approach is more accurate than other existing methods for identifying candidate glossary terms; this makes it less likely that our approach will miss important glossary terms. (2) Clustering provides an effective basis for grouping related terms; this makes clustering a useful support tool for selection of glossary terms and associating these terms with their related terms.
Interactions between the YycFG and PhoPR two‐component systems in Bacillus subtilis: the PhoR kinase phosphorylates the non‐cognate YycF response regulator upon phosphate limitation

Two‐component signal transduction systems (TCS) are an important mechanism by which bacteria sense and respond to their environment. Although each two‐component system appears to detect and respond to a specific signal(s), it is now evident that they do not always act independently of each other. In this paper we present data indicating regulatory links between the PhoPR two‐component system that participates in the cellular response to phosphate limitation, and the essential YycFG two‐component system in Bacillus subtilis. We show that the PhoR sensor kinase can activate the YycF response regulator during a phosphate limitation‐induced stationary phase, and that this reaction occurs in the presence of the cognate YycG sensor kinase. Phosphorylation of YycF by PhoR also occurs in vitro, albeit at a reduced level. However, the reciprocal cross‐phosphorylation does not occur. A second level of interaction between PhoPR and YycFG is indicated by the fact that cells depleted for YycFG have a severely deficient PhoPR‐dependent phosphate limitation response and that YycF can bind directly to the promoter of the phoPR operon. YycFG‐depleted cells neither activate expression of phoA and phoPR nor repress expression of the essential tagAB and tagDEF operons upon phosphate limitation. This effect is specific to the PhoPR‐dependent phosphate limitation response because PhoPR‐independent phosphate limitation responses can be initiated in YycFG‐depleted cells.
Renal 20-HETE inhibition attenuates changes in renal hemodynamics induced by L-NAME treatment in pregnant rats.

We previously reported that inhibition of nitric oxide (NO) synthesis by N-nitro-L-arginine methyl ester (L-NAME) during late pregnancy leads to increased production of renal vascular 20-hydroxyeicosatetraenoic acid (20-HETE), a cytochrome P-450 (CYP) 4A-derived vasoconstrictor, in pregnant rats. However, the effect of upregulation of vascular 20-HETE production on renal function after NO inhibition is not known. To test the hypothesis that increased gestational vascular 20-HETE synthesis after NO inhibition is involved in mediating blood pressure and renal functional changes, we first determined the IC(50) value of the effect of nitroprusside (SNP), a NO donor, on renal 20-HETE production in cortical microsomes. We then divided pregnant rats and age-matched virgin rats into a vehicle control group, an L-NAME treatment group (0.25 mg/ml in drinking water), and a group treated with L-NAME plus N-methylsulfonyl-12,12-dibromododec-11-enamide (DDMS; CYP4A-selective inhibitor, 10 mg.kg(-1). day(-1) iv). After 4 days of treatment, we measured blood pressure, renal blood flow (RBF), renal vascular resistance (RVR), and glomerular filtration rate (GFR) in each group. The addition of SNP (IC(50) = 22 microM) decreased renal cortical 20-HETE production. In pregnant rats, L-NAME treatment led to significantly higher mean arterial pressure (MAP) and RVR, and lower RBF and GFR. Combined treatment with DDMS and L-NAME significantly attenuated the increases in MAP and RVR and the decrease in GFR, but not the reduction in RBF induced by L-NAME treatment. L-NAME and L-NAME plus DDMS had no significant impact on renal hemodynamics in virgin rats. In addition, chronic treatment with DDMS selectively inhibited cortical 20-HETE production without a significant effect on CYP4A expression in L-NAME-treated pregnant rats. In conclusion, NO effectively inhibits renal cortical microsomal 20-HETE production in female rats. In pregnant rats, the augmentation of renal 20-HETE production after NO inhibition is associated with increased MAP and RVR, whereas decreased GFR is negated by treatment of a selective and competitive CYP4A inhibitor. These results demonstrate that the interaction between renal 20-HETE and NO is important in the regulation of renal function and blood pressure in pregnant rats.
Predicting Mathematical Achievement and Mathematical Learning Disability with a Simple Screening Tool

The Number Sets Test was developed to assess the speed and accuracy with which children can identify and process quantities represented by Arabic numerals and object sets. The utility of this test for predicting mathematics achievement and risk for mathematical learning disability (MLD) was assessed for a sample of 223 children. A signal detection analysis of first grade Number Sets Test scores provided measures of children's sensitivity to number and their response bias. The sensitivity measure, d', but not the response bias measure was predictive of third grade mathematics achievement scores, above and beyond the influence of intelligence, working memory, and first grade achievement scores. Further analyses assessed the sensitivity and specificity of the test and revealed that first grade d' scores identified 2 out of 3 children diagnosed as MLD in third grade and correctly identified about 9 out of 10 children who were not at risk for MLD.
Histone Chaperone Asf1 Plays an Essential Role in Maintaining Genomic Stability in Fission Yeast

The histone H3-H4 chaperone Asf1 is involved in chromatin assembly (or disassembly), histone exchange, regulation of transcription, and chromatin silencing in several organisms. To investigate the essential functions of Asf1 in Schizosaccharomyces pombe, asf1-ts mutants were constructed by random mutagenesis using PCR. One mutant (asf1-33(ts)) was mated with mutants in 77 different kinase genes to identify synthetic lethal combinations. The asf1-33 mutant required the DNA damage checkpoint factors Chk1 and Rad3 for its survival at the restrictive temperature. Chk1, but not Cds1, was phosphorylated in the asf1-33 mutant at the restrictive temperature, indicating that the DNA damage checkpoint was activated in the asf1-33 mutant. DNA damage occured in the asf1-33 mutant, with degradation of the chromosomal DNA observed through pulse-field gel electrophoresis and the formation of Rad22 foci. Sensitivity to micrococcal nuclease in the asf1-33 mutant was increased compared to the asf1+ strain at the restrictive temperature, suggesting that asf1 mutations also caused a defect in overall chromatin structure. The Asf1-33 mutant protein was mislocalized and incapable of binding histones. Furthermore, histone H3 levels at the centromeric outer repeat region were decreased in the asf1-33 mutant and heterochromatin structure was impaired. Finally, sim3, which encodes a CenH3 histone chaperone, was identified as a strong suppressor of the asf1-33 mutant. Taken together, these results clearly indicate that Asf1 plays an essential role in maintaining genomic stability in S. pombe.
Xbp1, a stress-induced transcriptional repressor of the Saccharomyces cerevisiae Swi4/Mbp1 family

We have identified Xbp1 (XhoI site-binding protein 1) as a new DNA-binding protein with homology to the DNA-binding domain of the Saccharomyces cerevisiae cell cycle regulating transcription factors Swi4 and Mbp1. The DNA recognition sequence was determined by random oligonucleotide selection and confirmed by gel retardation and footprint analyses. The consensus binding site of Xbp1, GcCTCGA(G/A)G(C/A)g(a/g), is a palindromic sequence, with an XhoI restriction enzyme recognition site at its center. This Xbpl binding site is similar to Swi4/Swi6 and Mbp1/Swi6 binding sites but shows a clear difference from these elements in one of the central core bases. There are binding sites for Xbp1 in the G1 cyclin promoter (CLN1), but they are distinct from the Swi4/Swi6 binding sites in CLN1, and Xbp1 will not bind to Swi4/Swi6 or Mbp1/Swi6 binding sites. The XBP1 promoter contains several stress-regulated elements, and its expression is induced by heat shock, high osmolarity, oxidative stress, DNA damage, and glucose starvation. When fused to the LexA DNA-binding domain, Xbp1 acts as transcriptional repressor, defining it as the first repressor in the Swi4/Mbp1 family and the first potential negative regulator of transcription induced by stress. Overexpression of XBP1 results in a slow-growth phenotype, lengthening of G1, an increase in cell volume, and a repression of G1 cyclin expression. These observations suggest that Xbp1 may contribute to the repression of specific transcripts and cause a transient cell cycle delay under stress conditions.
A 680 nA ECG Acquisition IC for Leadless Pacemaker Applications

A sub- μW ECG acquisition IC is presented for a single-chamber leadless pacemaker applications. It integrates a low-power, wide dynamic-range ECG readout front end together with an analog QRS-complex extractor. To save ASIC power, a current-multiplexed channel buffer is introduced to drive a 7 b-to-10 b self-synchronized SAR ADC which utilizes 4 fF/unit capacitors. The ASIC consumes only 680nA and achieves CMRR >90 dB, PSRR >80 dB, an input-referred noise of 4.9 μVrms in a 130 Hz bandwidth, and has rail-to-rail DC offset rejection. Low-power heartbeat detections are evaluated with the help of the ASIC acquiring nearly 20,000 beats across 10 different records from the MIT-BIH arrhythmia database. In the presence of muscle noise, both the average Sensitivity (Se) and Positive Predictivity (PP) show more than 90% when the input SNR >6 dB.
Multiparametric Analysis of CLASP-Interacting Protein Functions during Interphase Microtubule Dynamics

ABSTRACT The microtubule (MT) plus-end tracking protein (+TIP) CLASP mediates dynamic cellular behaviors and interacts with numerous cytoplasmic proteins. While the influence of some CLASP interactors on MT behavior is known, a comprehensive survey of the proteins in the CLASP interactome as MT regulators is missing. Ultimately, we are interested in understanding how CLASP collaborates with functionally linked proteins to regulate MT dynamics. Here, we utilize multiparametric analysis of time-lapse MT +TIP imaging data acquired in Drosophila melanogaster S2R+ cells to assess the effects on individual microtubule dynamics for RNA interference-mediated depletion of 48 gene products previously identified to be in vivo genetic CLASP interactors. While our analysis corroborates previously described functions of several known CLASP interactors, its multiparametric resolution reveals more detailed functional profiles (fingerprints) that allow us to precisely classify the roles that CLASP-interacting genes play in MT regulation. Using these data, we identify subnetworks of proteins with novel yet overlapping MT-regulatory roles and also uncover subtle distinctions between the functions of proteins previously thought to act via similar mechanisms.
British Thoracic Society guidelines for the management of suspected acute pulmonary embolism

INTRODUCTION In 1997 the British Thoracic Society (BTS) published advice entitled “Suspected acute pulmonary embolism: a practical approach”. It was recognised that it would need updating within a few years. Subsequent publications in several areas (CT pulmonary angiography, D-dimer, clinical probability, low molecular weight heparin) now provide sufficient evidence to allow this advice to be updated as guidelines. All the relevant literature published from January 1997 to December 2002 was located by searching the Medline and EmBase databases; some were meta-analyses and some were evidence based practice guidelines. Relevant papers published before 1997 not referenced in the earlier document were also retrieved. As before, the text was compiled by members of the BTS on behalf of its Standards of Care Committee, with feedback from experts recommended by specialist societies and, as with the previous guideline, we approached international authorities who all readily agreed to comment on the drafts. We are indebted to these advisors. These guidelines supersede the 1997 document, but many of the earlier concepts remain relevant. Where allusions are made to the previous document, this is shown as the page number in curly brackets {S18}. Papers from that document are not cited in the reference list, which therefore refers almost exclusively to publications from 1997 onwards. A similar structure to that in the previous guideline has been used, comprising a reference section, summary of recommendations, and a practical section for junior doctors. It was decided that the updated guidelines would concentrate on suspected pulmonary embolism (PE) and only include deep vein thrombosis (DVT) where relevant, even though both are part of venous thromboembolism (VTE). Compared with DVT alone, PE is potentially more serious and has a differential diagnosis of other serious conditions; many hospitals have established local protocols for the diagnosis and treatment of DVT but not for suspected PE. Although VTE is common in hospitalised patients, recommendations on prophylaxis are beyond the scope of these guidelines. Each section of these guidelines is followed by recommendations, graded according to standard criteria. 3 The Appendix contains charts (with notes) designed to be modified, according to local consensus and facilities, for inclusion in hospital handbooks. Each acute hospital should consider implementing the recommendations summarised in the box. Suggested topics for local audit are: • adherence to agreed hospital protocol • appropriate use of D-dimer, particularly in the emergency department • adequacy of clinical information provided with imaging requests • patient outcomes.
Linear precoding via conic optimization for fixed MIMO receivers

In this paper, the problem of designing linear precoders for fixed multiple-input-multiple-output (MIMO) receivers is considered. Two different design criteria are considered. In the first, the transmitted power is minimized subject to signal-to-interference-plus-noise-ratio (SINR) constraints. In the second, the worst case SINR is maximized subject to a power constraint. It is shown that both problems can be solved using standard conic optimization packages. In addition, conditions are developed for the optimal precoder for both of these problems, and two simple fixed-point iterations are proposed to find the solutions that satisfy these conditions. The relation to the well-known uplink-downlink duality in the context of joint transmit beamforming and power control is also explored. The proposed precoder design is general, and as a special case, it solves the transmit rank-one beamforming problem. Simulation results in a multiuser system show that the resulting precoders can significantly outperform existing linear precoders.
KECK OBSERVATIONS OF 160 GAMMA-RAY BURST HOST GALAXIES

We present a preliminary data release from our multi-year campaign at Keck Observatory to study the host galaxies of a large sample of Swift-era gamma-ray bursts via multi-color ground-based optical imaging and spectroscopy. With over 160 targets observed to date (and almost 100 host detections, most of which have not previously been reported in the literature) our effort represents the broadest GRB host survey to date. While targeting was heterogeneous, our observations span the known diversity of GRBs including short bursts, long bursts, spectrally soft GRBs (XRFs), ultra-energetic GRBs, X-ray faint GRBs, dark GRBs, SN-GRBs, and other sub-classes. We also present a preview of our database (currently available online via a convenient web interface) including a catalog of multi-color photometry, redshifts and line ID’s. Final photometry and reduced imaging and spectra will be available in the near future.
Quadrotor attitude estimation using adaptive fading multiplicative EKF

This paper presents the implementation of an adaptive fading multiplicative extended Kalman filter (AFMEKF), applied to the problem of attitude estimation in the context of quadrotors. The extended Kalman filter is adapted for use with quaternions and made adaptive to account for inaccurate measurement information. Simulations have been conducted in order to validate the filter performance.
Belief Propagation for Error Correcting Codes and Lossy Compression Using Multilayer Perceptrons

The belief propagation (BP) based algorithm is investigated as a potential decoder for both of error correcting codes and lossy compression, which are based on non-monotonic tree-like multilayer perceptron encoders. We discuss that whether the BP can give practical algorithms or not in these schemes. The BP implementations in those kind of fully connected networks unfortunately shows strong limitation, while the theoretical results seems a bit promising. Instead, it reveals it might have a rich and complex structure of the solution space via the BP-based algorithms.
VirtualScan: a new compressed scan technology for test cost reduction

This work describes the VirtualScan technology for scan test cost reduction. Scan chains in a VirtualScan circuit are split into shorter ones and the gap between external scan ports and internal scan chains are bridged with a broadcaster and a compactor. Test patterns for a VirtualScan circuit are generated directly by one-pass VirtualScan ATPG, in which multi-capture clocking and maximum test compaction are supported. In addition, VirtualScan ATPG avoids unknown-value and aliasing effects algorithmically without adding any additional circuitry. The VirtualScan technology has achieved successful tape-outs of industrial chips and has been proven to be an efficient and easy-to-implement solution for scan test cost reduction.
A Charging Strategy for PV-Based Battery Switch Stations Considering Service Availability and Self-Consumption of PV Energy

The photovoltaic (PV)-based battery switch station (BSS) is one of typical integration systems to implement a solar-to-vehicle system. The charging strategy is important for the operation of the PV-based BSS. Generally, instant charging strategy for swapped electric vehicle (EV) batteries can keep the availability of battery-swapping service at a high level. However, it is always accompanied with the possibility of bringing a negative effect on the utilization of PV energy. The contribution of this paper is mainly on a novel charging strategy for the PV-based BSS considering the service availability and self-consumption of the PV energy. First, considering the features of the PV-based BSS, evaluation indexes for the operation performance are defined, including the availability of battery-swapping service, self-consumption of the PV energy, and operation profit. Second, the charging strategy is proposed, including a battery-swapping service model and a power distribution model. In order to guarantee the service availability, the battery-swapping service model is used to decide the lower limit of charging power based on short-term forecasting results of EV requirements. The power distribution model is obliged to dispatch the charging power supplied by the PV system and power grid. Finally, in the case study, the operation of the BSS is simulated with the instant charging strategy and the proposed strategy under different scenarios. From the analysis of results, the proposed strategy can effectively improve the self-consumption of PV energy with the premise of guaranteeing the availability of the battery-swapping service.