Miracle-dz/UniFAR-FTUs huggingface dataset:
Shewanella oneidensis MR-1 Utilizes both Sodium- and Proton-Pumping NADH Dehydrogenases during Aerobic Growth

ABSTRACT Shewanella oneidensis MR-1 is a metal-reducing bacterium with the ability to utilize many different terminal electron acceptors, including oxygen and solid-metal oxides. Both metal oxide reduction and aerobic respiration have been studied extensively in this organism. However, electron transport chain processes upstream of the terminal oxidoreductases have been relatively understudied in this organism, especially electron transfer from NADH to respiratory quinones. Genome annotation indicates that S. oneidensis MR-1 encodes four NADH dehydrogenases, a proton-translocating dehydrogenase (Nuo), two sodium ion-translocating dehydrogenases (Nqr1 and Nqr2), and an “uncoupling” dehydrogenase (Ndh), but none of these complexes have been studied. Therefore, we conducted a study specifically focused on the effects of individual NADH dehydrogenase knockouts in S. oneidensis MR-1. We observed that two of the single-mutant strains, the ΔnuoN and ΔnqrF1 mutants, exhibited significant growth defects compared with the wild type. However, the defects were minor and only apparent under certain growth conditions. Further testing of the ΔnuoN ΔnqrF1 double-mutant strain yielded no growth in minimal medium under oxic conditions, indicating that Nuo and Nqr1 have overlapping functions, but at least one is necessary for aerobic growth. Coutilization of proton- and sodium ion-dependent energetics has important implications for the growth of this organism in environments with varied pH and salinity, including microbial electrochemical systems. IMPORTANCE Bacteria utilize a wide variety of metabolic pathways that allow them to take advantage of different energy sources, and to do so with varied efficiency. The efficiency of a metabolic process determines the growth yield of an organism, or the amount of biomass it produces per amount of substrate consumed. This parameter has important implications in biotechnology and wastewater treatment, where low growth yields are often preferred to minimize the production of microbial biomass. In this study, we investigated respiratory pathways containing NADH dehydrogenases with varied efficiency (i.e., the number of ions translocated per NADH oxidized) in the metal-reducing bacterium Shewanella oneidensis MR-1. We observed that two different respiratory pathways are used concurrently, and at least one pathway must be functional for growth under oxic conditions.
Exploring the Encoding Layer and Loss Function in End-to-End Speaker and Language Recognition System

In this paper, we explore the encoding/pooling layer and loss function in the end-to-end speaker and language recognition system. First, a unified and interpretable end-to-end system for both speaker and language recognition is developed. It accepts variable-length input and produces an utterance level result. In the end-to-end system, the encoding layer plays a role in aggregating the variable-length input sequence into an utterance level representation. Besides the basic temporal average pooling, we introduce a self-attentive pooling layer and a learnable dictionary encoding layer to get the utterance level representation. In terms of loss function for open-set speaker verification, to get more discriminative speaker embedding, center loss and angular softmax loss is introduced in the end-to-end system. Experimental results on Voxceleb and NIST LRE 07 datasets show that the performance of end-to-end learning system could be significantly improved by the proposed encoding layer and loss function.
Linear Time-varying feedback Law for vehicles with Ackermann steering

In this paper, we propose an optimal state-feedback control law for addressing point stabilization and tracking problems of nonholonomic vehicles with Ackermann steering in a unified manner. Unlike other feedback controllers that perform dynamic linearization of vehicle models, the proposed optimal feedback controller provides the state-feedback control to the original nonlinear vehicle model for achieving excellent state-tracking performance. In addition, nonlinear control techniques suggested in the literature to date require that the desired trajectory of the robot is generated using persistently excited inputs. This may be too restrictive and non-realistic hypothesis to mimic a real scenario. Here, we address this issue by developing a smooth state-feedback control law that is formulated by modifying the classical Pontryagin’s minimum principle. The proposed control law can be applied for solving control problems of a general class of nonlinear affine systems. The proposed control scheme offers a modular solution to other control techniques for a large number of mobile robot applications. The theoretical results are validated through computer simulations.
Developmental Changes of the Photochemical Reflectance Index (PRI), Chlorophyll Fluorescence and Leaf Pigments Show the Adaptability of Trees to Local Environments

For plants growing in parks and along the roadsides of a city, the environmental and seasonal regulation of growth, or photosynthesis, is seldom assessed. The phenology of plants may differ due to varying environments, which may result in different growth or adaptability to local environments. Therefore, we explored several assays and optical indicators of photosynthesis and stress in three tree species (Prunus yedoensis Matsum, Zelkova serrata Makino and Acer palmatum Thunb. ) and two herbaceous species (Artemisia princeps Pamp and Taraxacum officinale Weber)growing commonly in three local parks of Changwon city, a large industrial city in Korea. The photochemical reflectance index (PRI), chlorophyll fluorescence, and pigments including chlorophyll and the flavonoids of leaves were monitored over a growing season for two years to evaluate the adaptability of plants to local environments. The values of all measurements exhibited striking seasonal and regional changes. PRI values were closely timed with photosynthetic activity and the pigment formation of leaves, particularly in some tree species. For the tree species, the plants which had the low values of PRI during the active growing season showed low levels of both chlorophyll fluorescence and high level of flavonoid, indicating that these plants were experiencing low photosynthetic activity and the specific needs in growth and development were not sufficiently provided by the local environment. Our results indicate that PRI provided a clear optical indicator of plant adaptability to the local environment and may provide a useful metric of effective growth using remote sensing measurements. Furthermore, the periodic PRI measurement is encouraged to be included in the surveillance program for city plant management.
Molecular and Ultrastructural Mechanisms Underlying Yellow Dwarf Symptom Formation in Wheat after Infection of Barley Yellow Dwarf Virus

Wheat (Tritium aestivum L.) production is essential for global food security. Infection of barley yellow dwarf virus-GAV (BYDV-GAV) results in wheat showing leaf yellowing and plant dwarfism symptom. To explore the molecular and ultrastructural mechanisms underlying yellow dwarf symptom formation in BYDV-GAV-infected wheat, we investigated the chloroplast ultrastructure via transmission electron microscopy (TEM), examined the contents of the virus, H2O2, and chlorophyll in Zhong8601, and studied the comparative transcriptome through microarray analyses in the susceptible wheat line Zhong8601 after virus infection. TEM images indicated that chloroplasts in BYDV-GAV-infected Zhong8601 leaf cells were fragmentized. Where thylakoids were not well developed, starch granules and plastoglobules were rare. Compared with mock-inoculated Zhong8601, chlorophyll content was markedly reduced, but the virus and H2O2 contents were significantly higher in BYDV-GAV-infected Zhong8601. The transcriptomic analyses revealed that chlorophyll biosynthesis and chloroplast related transcripts, encoding chlorophyll a/b binding protein, glucose-6-phosphate/phosphate translocator 2, and glutamyl-tRNA reductase 1, were down-regulated in BYDV-GAV-infected Zhong8601. Some phytohormone signaling-related transcripts, including abscisic acid (ABA) signaling factors (phospholipase D alpha 1 and calcineurin B-like protein 9) and nine ethylene response factors, were up-regulated. Additionally, reactive oxygen species (ROS)-related genes were transcriptionally regulated in BYDV-GAV infected Zhong8601, including three up-regulated transcripts encoding germin-like proteins (promoting ROS accumulation) and four down-regulated transcripts encoding peroxides (scavenging ROS). These results clearly suggest that the yellow dwarf symptom formation is mainly attributed to reduced chlorophyll content and fragmentized chloroplasts caused by down-regulation of the chlorophyll and chloroplast biosynthesis related genes, ROS excessive accumulation, and precisely transcriptional regulation of the above-mentioned ABA and ethylene signaling- and ROS-related genes in susceptible wheat infected by BYDV-GAV.
6‐Minute walk test predicts prolonged hospitalization in patients undergoing transcatheter mitral valve repair by MitraClip

The 6‐minute walk test (6MWT) is a simple functional test that can predict exercise capacity and is widely employed to assess treatment outcomes. Although mortality with transcatheter mitral valve repair (TMVr) using the MitraClip (Abbott Vascular, Menlo Park, CA) is significantly less than for open mitral valve surgery in high‐risk patients, identifying which patient will benefit the most from TMVr remains a concern. There are limited prognostic metrics guiding patient selection and, no studies have reported relationship between prolonged hospitalization and 6MWT. This study aimed to determine if the 6MWT can predict prolonged hospitalization in patients undergoing TMVr by MitraClip.
Deep Neural Network Based Supervised Speech Segregation Generalizes to Novel Noises through Large-scale Training

Abstract : Deep neural network (DNN) based supervised speech segregation has been successful in improving human speech intelligibility in noise, especially when DNN is trained and tested on the same noise type. A simple and effective way for improving generalization is to train with multiple noises. This letter demonstrates that by training with a large number of different noises, the objective intelligibility results of DNN based supervised speech segregation on novel noises can match or even outperform those on trained noises. This demonstration has an important implication that improving human speech intelligibility in unknown noisy environments is potentially achievable.
The improvement of page sorting algorithm for music users in Nutch

The default page sorting algorithm in Nutch which is open source search engine is TF/IDF algorithm, but it's difficult to meet the demand of music page sorting. The paper presents a new page sorting algorithm bases on BM25 model for music users. According word count and keyword frequency in music web pages, the pages whose keyword frequency is high and text size is long such as music home page, can be sorted at or near the top, and other music pages are low in sorting. The experiment proved that the new algorithm bases on BM25 model is better to meet demand of music page sorting than TF/IDF algorithm for music users.
Compensatory Actions of Ldb Adaptor Proteins During Corticospinal Motor Neuron Differentiation

Abstract Although many genes that specify neocortical projection neuron subtypes have been identified, the downstream effectors that control differentiation of those subtypes remain largely unknown. Here, we demonstrate that the LIM domain‐binding proteins Ldb1 and Ldb2 exhibit dynamic and inversely correlated expression patterns during cerebral cortical development. Ldb1‐deficient brains display severe defects in proliferation and changes in regionalization, phenotypes resembling those of Lhx mutants. Ldb2‐deficient brains, on the other hand, exhibit striking phenotypes affecting layer 5 pyramidal neurons: Immature neurons have an impaired capacity to segregate into mature callosal and subcerebral projection neurons. The analysis of Ldb2 single‐mutant mice reveals a compensatory role of Ldb1 for Ldb2 during corticospinal motor neuron (CSMN) differentiation. Animals lacking both Ldb1 and Ldb2 uncover the requirement for Ldb2 during CSMN differentiation, manifested as incomplete CSMN differentiation, and ultimately leading to a failure of the corticospinal tract.
Development of an Avirulent Salmonella Surrogate for Modeling Pathogen Behavior in Pre- and Postharvest Environments

ABSTRACT Recurrent outbreaks of bacterial gastroenteritis linked to the consumption of fresh fruits and vegetables highlight the paucity of understanding of the ecology of Salmonella enterica under crop production and postharvest conditions. These gaps in knowledge are due, at least in part, to the lack of suitable surrogate organisms for studies for which biosafety level 2 is problematic. Therefore, we constructed and validated an avirulent strain of Salmonella enterica serovar Typhimurium. The strain lacks major Salmonella pathogenicity islands SPI-1, SPI-2, SPI-3, SPI-4, and SPI-5 as well as the virulence plasmid pSLT. Deletions and the absence of genomic rearrangements were confirmed by genomic sequencing, and the surrogate behaved like the parental wild-type strain on selective media. A loss-of-function (phoN) selective marker allowed the differentiation of this strain from wild-type strains on a medium containing a chromogenic substrate for alkaline phosphatase. Lack of virulence was confirmed by oral infection of female BALB/c mice. The strain persisted in tomatoes, cantaloupes, leafy greens, and soil with the same kinetics as the parental wild-type and selected outbreak strains, and it reached similar final population levels. The responses of this strain to heat treatment and disinfectants were similar to those of the wild type, supporting its potential as a surrogate for future studies on the ecology and survival of Salmonella in production and processing environments. IMPORTANCE There is significant interest in understanding the ecology of human pathogens in environments outside of their animal hosts, including the crop production environment. However, manipulative field experiments with virulent human pathogens are unlikely to receive regulatory approval due to the obvious risks. Therefore, we constructed an avirulent strain of S. enterica serovar Typhimurium and characterized it extensively.
Stereotactic body radiation therapy for palliative management of pancreatic adenocarcinoma in elderly and medically inoperable patients

Stereotactic body radiation therapy (SBRT) represents a promising treatment option for patients with localized pancreatic ductal adenocarcinoma (PDAC) who cannot tolerate surgical therapy. We retrospectively reviewed the records of patients with localized PDAC treated with SBRT at our institution between 2010 and 2016 to identify patients deemed medically inoperable due to poor performance status, advanced age, and/or comorbid conditions. Overall survival (OS), progression-free survival (PFS), and local progression-free survival (LPFS) were estimated using Kaplan-Meier curves. Twenty-nine patients were included. Median age was 74 (IQR 68-79). Thirteen patients (45%) had an Eastern Cooperative Oncology Group performance status of 2. Six patients (19%) had chronic obstructive pulmonary disease, 9 (31%) had cardiovascular disease, and 17 (58%) had diabetes mellitus. SBRT was delivered over 5 fractions to a median dose of 28 Gy (IQR, 25-33). Twenty-two patients (76%) received induction chemotherapy prior to SBRT, and 9 (31%) received maintenance chemotherapy after SBRT. Median OS was 13 months from diagnosis. Median OS and PFS were 8 and 6 months from SBRT, respectively. Six and 12-month LPFS rates were 91% and 78%, respectively. Patients receiving induction chemotherapy had superior survival from diagnosis than those who did not (14 vs. 7 months, p = 0.01). Three patients (10%) experienced acute grade ≥3 toxicity, and 1 patient (4%) experienced grade ≥3 late toxicity. Symptom relief was achieved at three-month follow-up in 8 of 11 patients (73%) experiencing abdominal pain. These results suggest SBRT may be safe and effective for patients who cannot tolerate surgery.
Green Synthesis of Silver Nanoparticles: Eco-Friendly and Antibacterial

Silver nanoparticles are one of the most widely applicable particles whose application is increasing in Nano world daily. In this paper the Lens culinaris seed extract was assessed for thegreen synthesis of silvernanoparticlesat temperature of 25 ◦ C. The nanoparticles were characterized using Inductively Coupled Plasma spectrometry (ICP), X-ray diffraction (XRD) and Transmission electron microscopy (TEM). Then the antimicrobial activities of these nanoparticles were investigated. P. aeruginosa and S aureus were used as representatives of Gram-negative and Gram-positive bacteria, respectively. Percentage conversion of metal ion to metal nanoparticles were more than 95% after 60 days of the reaction. XRD was used to confirm the crystalline nature of the particles. Silver nanoparticles were mostly spherical with range in size from 5-25 nm. Ag nanoparticles synthesized with extract were exhibited a strong antibacterial activity against bothP.aeruginosa and S.aureus. This process is completely green and eco-friendly compatible.
Graphene-based wearable temperature sensor and infrared photodetector on a flexible polyimide substrate

This paper describes an approach to the fabrication of flexible electronics i.e., a wearable temperature sensor and infrared (IR) photodetector on flexible polyimide (PI) substrate. Solar exfoliated reduced graphene oxide (SrGO) and graphene flakes are used as the sensing materials for developing the sensors on a PI substrate. PI, apart from being flexible and compatible with microfabrication processes, also helps in reducing the mobility and recombination of the photo-generated electrons of graphene due of its dielectric nature, thus enabling IR detection. Current responsivity and external quantum efficiency of IR photodetector for graphene flake- and SrGO-based devices were found to be 0.4 A W−1, 16.53% and 0.8 A W−1, 33.06% respectively which are higher than those of commercially available photodetectors. In addition, we demonstrate an ultrasensitive wearable human body temperature sensor in the temperature range of 35 °C to 45 °C, wherein both graphene flake- and SrGO-based devices exhibited a negative temperature coefficient of −41.30 × 10−4 °C−1 and −74.29 × 10−4 °C−1 respectively, which are higher than commercially available counterparts. Plausible underlying mechanisms to both IR sensing and temperature sensing have been studied. Furthermore, as a proof of concept, we investigated the effect of IR radiation emitted by a human hand on the device. Interestingly it was found that the device was very sensitive to it, indicating that the sensor can be used for motion detection which has potential applications in security, surveillance etc. The strategy presented here provides a new, simple, cost effective approach for the fabrication of next-generation wearable and bio-implantable devices based on a polyimide substrate that can be easily integrated onto the surface of a leaf, skin, paper, clothes etc owing to its versatile nature.
Cannabinoid CB2 Receptors Regulate Central Sensitization and Pain Responses Associated with Osteoarthritis of the Knee Joint

Osteoarthritis (OA) of the joint is a prevalent disease accompanied by chronic, debilitating pain. Recent clinical evidence has demonstrated that central sensitization contributes to OA pain. An improved understanding of how OA joint pathology impacts upon the central processing of pain is crucial for the identification of novel analgesic targets/new therapeutic strategies. Inhibitory cannabinoid 2 (CB2) receptors attenuate peripheral immune cell function and modulate central neuro-immune responses in models of neurodegeneration. Systemic administration of the CB2 receptor agonist JWH133 attenuated OA-induced pain behaviour, and the changes in circulating pro- and anti-inflammatory cytokines exhibited in this model. Electrophysiological studies revealed that spinal administration of JWH133 inhibited noxious-evoked responses of spinal neurones in the model of OA pain, but not in control rats, indicating a novel spinal role of this target. We further demonstrate dynamic changes in spinal CB2 receptor mRNA and protein expression in an OA pain model. The expression of CB2 receptor protein by both neurones and microglia in the spinal cord was significantly increased in the model of OA. Hallmarks of central sensitization, significant spinal astrogliosis and increases in activity of metalloproteases MMP-2 and MMP-9 in the spinal cord were evident in the model of OA pain. Systemic administration of JWH133 attenuated these markers of central sensitization, providing a neurobiological basis for analgesic effects of the CB2 receptor in this model of OA pain. Analysis of human spinal cord revealed a negative correlation between spinal cord CB2 receptor mRNA and macroscopic knee chondropathy. These data provide new clinically relevant evidence that joint damage and spinal CB2 receptor expression are correlated combined with converging pre-clinical evidence that activation of CB2 receptors inhibits central sensitization and its contribution to the manifestation of chronic OA pain. These findings suggest that targeting CB2 receptors may have therapeutic potential for treating OA pain.
Efficient Scheduling of Serial Iterative Decoding for Zigzag Decodable Fountain Codes

Fountain codes are erasure correcting codes realizing reliable communication systems for the multicast on the Internet. The zigzag decodable fountain (ZDF) code is one of generalization of the Raptor code, i.e, applying shift operation to generate the output packets. The ZDF code is decoded by a two-stage iterative decoding algorithm, which combines the packet-wise peeling algorithm and the bit-wise peeling algorithm. By the bit-wise peeling algorithm and shift operation, ZDF codes outperform Raptor codes under iterative decoding in terms of decoding erasure rates and overheads. However, the bit-wise peeling algorithm spends long decoding time. This paper proposes a fast bit-wise decoding algorithm for the ZDF codes. Simulation results show that the proposed algorithm drastically reduces the decoding time compared with the existing algorithm.