Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Importance of the Interhelical Hydrogen Bond between Thr204 and Tyr174 of Sensory Rhodopsin II and Its Alteration during the Signaling Process*

Sensory rhodopsin II (SRII), a receptor for negative phototaxis in haloarchaea, transmits light signals through changes in protein-protein interaction with its transducer HtrII. Light-induced structural changes throughout the SRII-HtrII interface, which spans the periplasmic region, membrane-embedded domains, and cytoplasmic domains near the membrane, have been identified by several studies. Here we demonstrate by site-specific mutagenesis and analysis of phototaxis behavior that two residues in SRII near the membrane-embedded interface (Tyr174 on helix F and Thr204 on helix G) are essential for signaling by the SRII-HtrII complex. These residues, which are the first in SRII shown to be required for phototaxis function, provide biological significance to the previous observation that the hydrogen bond between them is strengthened upon the formation of the earliest SRII photointermediate (SRIIK) only when SRII is complexed with HtrII. Here we report frequency changes of the S-H stretch of a cysteine substituted for SRII Thr204 in the signaling state intermediates of the SRII photocycle, as well as an influence of HtrII on the hydrogen bond strength, supporting a direct role of the hydrogen bond in SRII-HtrII signal relay chemistry. Our results suggest that the light signal is transmitted to HtrII from the energized interhelical hydrogen bond between Thr204 and Tyr174, which is located at both the retinal chromophore pocket and in helices F and G that form the membrane-embedded interaction surface to the signal-bearing second transmembrane helix of HtrII. The results argue for a critical process in signal relay occurring at this membrane interfacial region of the complex.
Heterogeneous Concurrent Modeling and Design R S I T Y @bullet O F @bullet C Overview of the Ptolemy Project 1. Modeling and Design

The Ptolemy project studies heterogeneous modeling and design of concurrent systems. The focus is on embedded systems, particularly those that mix technologies, including for example analog and digital electronics, hardware and software, and electronics and mechanical devices (including MEMS, microelectromechanical systems). The focus is also on systems that are complex in the sense that they mix widely different operations, such as signal processing, feedback control, sequential decision making , and user interfaces. Modeling is the act of representing a system or subsystem formally. A model might be mathematical , in which case it can be viewed as a set of assertions about properties of the system such as its func-tionality or physical dimensions. A model can also be constructive, in which case it defines a computational procedure that mimics a set of properties of the system. Constructive models are often used to describe behavior of a system in response to stimulus from outside the system. Constructive models are also called executable models. Design is the act of defining a system or subsystem. Usually this involves defining one or more models of the system and refining the models until the desired functionality is obtained within a set of constraints. Design and modeling are obviously closely coupled. In some circumstances, models may be immutable, in the sense that they describe subsystems, constraints, or behaviors that are externally imposed on a design. For instance, they may describe a mechanical system that is not under design, but must be controlled by an electronic system that is under design. Executable models are sometimes called simulations, an appropriate term when the executable model is clearly distinct from the system it models. However, in many electronic systems, a model that starts as a simulation mutates into a software implementation of the system. The distinction between the model and the system itself becomes blurred in this case. This is particularly true for embedded software. Embedded software is software that resides in devices that are not first-and-foremost computers.
STC-TIMIT: Generation of a Single-channel Telephone Corpus

This paper describes a new speech corpus, STC-TIMIT, and discusses the process of design, development and its distribution through LDC. The STC-TIMIT corpus is derived from the widely used TIMIT corpus by sending it through a real and single telephone channel. TIMIT is phonetically balanced, covers the dialectal diversity in continental USA and has been extensively used as a benchmark for speech recognition algorithms, especially in early stages of development. The experimental usability of TIMIT has been increased eventually with the creation of derived corpora, passing the original data through different channels. One such example is the well-known NTIMIT corpus, where the original files in TIMIT are re-recorded after being sent through different telephone calls, resulting in a corpus that characterizes telephone channels in a wide sense. In STC-TIMIT, we followed a similar procedure, but the whole corpus was transmitted in a single telephone call with the goal of obtaining data from a real and yet highly stable telephone channel across the whole corpus. Files in STC-TIMIT are aligned to those of TIMIT with a theoretical precision of 0.125 ms, making TIMIT labels valid for the new corpus. The experimental section presents several results on speech recognition accuracy.
Consumption of Dairy Products and Colorectal Cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC)

Background Prospective studies have consistently reported lower colorectal cancer risks associated with higher intakes of total dairy products, total milk and dietary calcium. However, less is known about whether the inverse associations vary for individual dairy products with differing fat contents. Materials and Methods In the European Prospective Investigation into Cancer and Nutrition (EPIC), we investigated the associations between intakes of total milk and milk subtypes (whole-fat, semi-skimmed and skimmed), yoghurt, cheese, and dietary calcium with colorectal cancer risk amongst 477,122 men and women. Dietary questionnaires were administered at baseline. Multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards models, adjusted for relevant confounding variables. Results During the mean 11 years of follow-up, 4,513 incident cases of colorectal cancer occurred. After multivariable adjustments, total milk consumption was inversely associated with colorectal cancer risk (HR per 200 g/day 0.93, 95% CI: 0.89–0.98). Similar inverse associations were observed for whole-fat (HR per 200 g/day 0.90, 95% CI: 0.82–0.99) and skimmed milk (HR per 200 g/day 0.90, 95% CI: 0.79–1.02) in the multivariable models. Inverse associations were observed for cheese and yoghurt in the categorical models; although in the linear models, these associations were non-significant. Dietary calcium was inversely associated with colorectal cancer risk (HR per 200 mg/day 0.95, 95% CI: 0.91–0.99); this association was limited to dairy sources of calcium only (HR per 200 mg/day 0.95, 95% CI: 0.91–0.99), with no association observed for non-dairy calcium sources (HR per 200 mg/day 1.00, 95% CI: 0.81–1.24). Conclusions Our results strengthen the evidence for a possible protective role of dairy products on colorectal cancer risk. The inverse associations we observed did not differ by the fat content of the dairy products considered.
Multi-Task Learning in Conditional Random Fields for Chunking in Shallow Semantic Parsing

Alternating Structure Optimization (ASO) is a recently proposed linear Multitask Learning algorithm. Although its effective has been verified in both semi-supervised as well as supervised methods, yet they necessitate taking external resource as a prerequisite. Therefore, feasibility of employing ASO to further improve the performance merely rests on the labeled data on hand proves to be a task deserving close scrutiny. Catering to this challenging while untapped problem, this paper presents a novel application of ASO to the subtask of Shallow Semantic Parsing: Chunking. Our experiments on Chinese Treebank 5.0 present promising result in chunk analysis, and the error rate is reduced by 5.72%, proposing a profound way to further improve the performance.
An Arabidopsis Purple Acid Phosphatase with Phytase Activity Increases Foliar Ascorbate1[OA]

Ascorbate (AsA) is the most abundant antioxidant in plant cells and a cofactor for a large number of key enzymes. However, the mechanism of how AsA levels are regulated in plant cells remains unknown. The Arabidopsis (Arabidopsis thaliana) activation-tagged mutant AT23040 showed a pleiotropic phenotype, including ozone resistance, rapid growth, and leaves containing higher AsA than wild-type plants. The phenotype was caused by activation of a purple acid phosphatase (PAP) gene, AtPAP15, which contains a dinuclear metal center in the active site. AtPAP15 was universally expressed in all tested organs in wild-type plants. Overexpression of AtPAP15 with the 35S cauliflower mosaic virus promoter produced mutants with up to 2-fold increased foliar AsA, 20% to 30% decrease in foliar phytate, enhanced salt tolerance, and decreased abscisic acid sensitivity. Two independent SALK T-DNA insertion mutants in AtPAP15 had 30% less foliar AsA and 15% to 20% more phytate than wild-type plants and decreased tolerance to abiotic stresses. Enzyme activity of partially purified AtPAP15 from plant crude extract and recombinant AtPAP15 expressed in bacteria and yeast was highest when phytate was used as substrate, indicating that AtPAP15 is a phytase. Recombinant AtPAP15 also showed enzyme activity on the substrate myoinositol-1-phosphate, indicating that the AtPAP15 is a phytase that hydrolyzes myoinositol hexakisphosphate to yield myoinositol and free phosphate. Myoinositol is a known precursor for AsA biosynthesis in plants. Thus, AtPAP15 may modulate AsA levels by controlling the input of myoinositol into this branch of AsA biosynthesis in Arabidopsis.
A practical viewpoint on the performance of LDPC codes over the fast Rayleigh fading wire-tap channel

In this paper, we carry out a practical assessment of the performance of finite-length LDPC codes over the wiretap channel with fast Rayleigh fading. Classical metrics for physical layer security, like the secrecy capacity, are based on information theoretic arguments, and provide the ultimate security bounds for these schemes. However, it is difficult to design practical schemes, using some specific finite-length code, able to approach such a performance. Then we use a more practical metric, based on the error probability, which allows assessing the performance achieved in terms of both reliability and security over the fast Rayleigh fading wire-tap channel.
A dried blood spot mass spectrometry metabolomic approach for rapid breast cancer detection

Objective Breast cancer (BC) is still a lethal threat to women worldwide. An accurate screening and diagnosis strategy performed in an easy-to-operate manner is highly warranted in clinical perspective. Besides the routinely focused protein markers, blood is full of small molecular metabolites with diverse structures and properties. This study aimed to screen metabolite markers with BC diagnosis potentials. Methods A dried blood spot-based direct infusion mass spectrometry (MS) metabolomic analysis was conducted for BC and non-BC differentiation. The targeted analytes included 23 amino acids and 26 acylcarnitines. Results Multivariate analysis screened out 21 BC-related metabolites in the blood. Regression analysis generated a diagnosis model consisting of parameters Pip, Asn, Pro, C14:1/C16, Phe/Tyr, and Gly/Ala. Tested with another set of BC and non-BC samples, this model showed a sensitivity of 92.2% and a specificity of 84.4%. Compared to the routinely used protein markers, this model exhibited distinct advantage with its higher sensitivity. Conclusion Blood metabolites screening is a more plausible approach for BC detection. Furthermore, this direct MS analysis could be finished within few minutes, which means that its throughput is higher than the currently used imaging techniques.
In silico modeling for Identification of promising antimicrobials of Herbal origin against highly virulent pathogenic strains of bacteria like New Delhi Metallo-beta-lactamase -1 Escherichia coli

Drug resistance has mushroomed up after advent of every major class of antimicrobial drugs, varying in time from as short as 1 year (penicillin) to >10 years. Organisms associated with nosocomial and community acquired infections are also becoming drug resistant due to the over utilization of antibiotics, consequently leading to high morbidity, mortality and increased health costs. One such example of a beta lactamase producing bacteria is New Delhi Metallo beta lactamase (NDM-1) producing Escherichia coli and Klebsiella pneumoniae, and was reported for the first time in the year 2009 in a Swedish patient. NDM-1 bacterial strains possess more potent hydrolysis ability towards almost all antibiotics, including Carbapenems. NDM-1 bacterial strains are sensitive to Tigecycline and Colistin but there is problem of side effects associated with them. In such a situation where NDM-1 strains are displacing antibiotic sensitive strains and are resistant to most of the chemotherapeutic agents, there is a need for the search of novel alternative effective therapeutic agents. The present bioprospective study aims to analyze the potential of various natural plants or their products, based upon bioactivity parameters and presence of chemical constituents, using matrix based modeling, followed by optimization. The outcomes of the lead identification need verification with respect to antimicrobial potential against virulent NDM-1 Escherichia coli.
Resilient Capacity-Aware Multicast Based on Overlay Networks

The global deployment of IP multicast has been slow due to the difficulties related to heterogeneity, scalability, manageability, and lack of a robust inter-domain multicast routing protocol. Application-level multicast becomes a promising alternative. Many overlay multicast systems have been proposed in recent years. However, they are insufficient in supporting applications that require large-scale any-source multicast with highly varied host capacities and highly dynamic membership. In this paper, we propose two capacity-aware multicast systems that focus on host heterogeneity, dynamic membership, scalability, and any source multicast. We extend Chord and Koorde to be capacity-aware. We then embed implicit degree-varying multicast trees on top of the overlay network and develop multicast routines that automatically follow the trees to disseminate multicast messages. The implicit trees are well balanced with workload evenly spread across the network. We also perform extensive simulations to evaluate the proposed multicast systems
Optimal indicators for microtopography-oriented soil quality assessment in semiarid regions of the Loess Plateau, China.

This study was aimed to identify optimal indicators for microtopography-oriented soil quality assessment. Twenty-two soil physicochemical and biological parameters were investigated at 93 sampling points in five different microtopographic units in semiarid regions of the Loess Plateau, where the principal functions of eroded agriculture soils are related to productivity and anti-erosion ability. The selection of soil quality indicators was accomplished using a combination of sensitivity analysis, principal component analysis, and stepwise regression. The indicators used for microtopographyoriented soil quality assessment were found to be moderately sensitive with no high sensitivity. Moderately sensitive soil quality indicators including the levels of sucrase activity (SA), available phosphorus (AP), total nitrogen (TN), soil organic matter (SOM), and urease (UA) are the major objectives of soil quality restoration and regulation in the study area. The 22 soil physicochemical and biological parameters indicative of soil quality were grouped into seven soil quality factors; SOM, water-holding capacity, total phosphorous (TP), total potassium (TK), soil water content, capillary porosity, and AP. Optimal indicators for microtopography-oriented soil quality assessment in the study area were identified as; SOM, TN, SA, UA, AP, TP, CaCO3, APA, and TK. Among these, the SOM level was the key indicator for characterizing soil quality in relation to microtopography in the semiarid loess region. This study provides reference information for the conservation of agricultural soils and improvement of low-yield farmlands in semiarid regions of the Loess Plateau. This will enable better agricultural decisions by the residents and aid decision making by the government according to local conditions.
Pituitary adenomas and craniopharyngiomas.

Pituitary adenomas and craniopharyngiomas are similar in some aspects. Usually, they both are histologically benign, slow-growing intracranial tumors that arise in the sellar and parasellar areas, and tend to cause similar symptoms and signs, such as, but not limited to, progressive visual loss, progressive endocrine problems, and headache. They both are likely to have an excellent prognosis if they are suitably treated with surgical management and occasionally with adjunctive medical or radiotherapeutic procedures, including radiosurgery (30).
Identification of Wake-Active Dopaminergic Neurons in the Ventral Periaqueductal Gray Matter

Recent evidence suggests that dopamine plays an important role in arousal, but the location of the dopaminergic neurons that may regulate arousal remains unclear. It is sometimes assumed that the dopaminergic neurons in the ventral tegmental area that project to the prefrontal cortex and striatum may regulate the state of arousal; however, the firing of these dopaminergic neurons does not correlate with overall levels of behavioral wakefulness. We identified wake-active dopaminergic neurons by combining immunohistochemical staining for Fos and tyrosine hydroxylase (TH) in awake and sleeping rats. Approximately 50% of the TH-immunoreactive (TH-ir) cells in the ventral periaqueductal gray matter (vPAG) expressed Fos protein during natural wakefulness or wakefulness induced by environmental stimulation, but none expressed Fos during sleep. Fos immunoreactivity was not seen in the substantia nigra TH-immunoreactive cells in either condition. Injections of 6-hydroxydopamine into the vPAG, which killed 55–65% of wake-active TH-ir cells but did not injure nearby serotoninergic cells, increased total daily sleep by ∼20%. By combining retrograde and anterograde tracing, we showed that these wake-active dopaminergic cells have extensive reciprocal connections with the sleep–wake regulatory system. The vPAG dopaminergic cells may provide the long-sought ascending dopaminergic waking influence. In addition, their close relationship with the dorsal raphe nucleus will require reassessment of previous studies of the role of the dorsal raphe nucleus in sleep, because many of those experiments may have been confounded by the then-unrecognized presence of intermingled wake-active dopaminergic neurons.
Assessment of bone in Ehlers Danlos syndrome by ultrasound and densitometry

OBJECTIVE Ehlers Danlos syndrome (EDS) is an inherited disorder of connective tissue characterised by hyperextensible skin, joint laxity, and easy bruising. There are phenotypic similarities with osteogenesis imperfecta, but in EDS a tendency to fracture or altered bone mass has not previously been considered to be a cardinal feature. METHOD This case-control design study investigates whether 23 patients with EDS had differences in fracture rates, bone mass, and calcaneal ultrasound parameters compared with age and sex matched controls. RESULTS 23 cases of EDS (mean (SD) age 38.5 (15.5)) were compared with 23 controls (mean age 37.8 (14.5)). A significant reduction in bone density measured by dual energyx ray absorptiometry was found at the neck of femur by 0.9 SD, p = 0.05, and lumbar spine by 0.74 SD, p = 0.02. At the calcaneum, broad band ultrasound attenuation and speed of sound were significantly reduced compared with controls by 0.95 SD (p = 0.004) and 0.49 SD (p = 0.004) for broad band ultrasound attenuation and speed of sound respectively. Broad band ultrasound attenuation and speed of sound remained significantly reduced after adjusting for bone mineral density (BMD). After adjusting for functional status (HAQ), age and sex, hypermobility was inversely correlated with broad band ultrasound attenuation and SOS, but not BMD at hip or spine. Previous fracture was 10 times more common in EDS (p < 0.001), with 86.9% of patients reporting a total of 47 low impact fractures, compared with 8.7% of controls. CONCLUSION This study has identified a tendency of EDS patients to fracture, have low bone mass and abnormal bone structure. The aetiology is likely to be multifactorial, with an inherited structural element, accentuated by immobility or reduced exercise. This is one of the first clinical studies to suggest ultrasound can detect structural differences in bone, independent of dual energy x ray absorptiometry.
Modeling prosodic dynamics for speaker recognition

Most current state-of-the-art automatic speaker recognition systems extract speaker-dependent features by looking at short-term spectral information. This approach ignores long-term information that can convey supra-segmental information, such as prosodics and speaking style. We propose two approaches that use the fundamental frequency and energy trajectories to capture long-term information. The first approach uses bigram models to model the dynamics of the fundamental frequency and energy trajectories for each speaker. The second approach uses the fundamental frequency trajectories of a predefined set of words as the speaker templates and then, using dynamic time warping, computes the distance between the templates and the words from the test message. The results presented in this work are on Switchboard I using the NIST Extended Data evaluation design. We show that these approaches can achieve an equal error rate of 3.7%, which is a 77% relative improvement over a system based on short-term pitch and energy features alone.
Ultra-high resolution atmospheric global circulation model NICAM on graphics processing unit

Abstract— Climate simulations have significant role in analyzing changes that have occurred in the Earth, give us better understanding of the recently happened processes. Most of the existing models perform approximate results and fundamental improvements of the software models are necessary to increase accuracy. We present an efficient implementation of ultra-high resolution atmospheric global circulation model on graphics processing units(GPUs). The model based on the nonhydrostatic system with the icosahedral grid and called "NICAM". We ported computationally intensive part of the NICAM code to GPU by using CUDA FORTRAN, then validated and compared its GPU performance to that for the parallel CPU version of the code. This approach shows a good performance results together with reducing memory consumption compared to a fully GPU approaches. Our results show 5x speedup for a computationally intensive part of shallow water simulation model on a single GPU in comparison with a parallel CPU implementation (5 cores).