Miracle-dz/UniFAR-FTUs huggingface dataset:
Building bridges between cellular and molecular structural biology

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures. DOI: http://dx.doi. org/10.7554/eLife.25835. 001
Data compression using multiple videos for photo-based augmented reality system

A photo-based augmented reality (Photo AR) system is an AR system that uses photographic images, instead of computer graphics of 3D models. The advantage of this system is that it can display realistic augmented views to users; however, it requires large disk-space volumes because it uses many images. The images can be compressed by storing in video formats; however, the rendering times of the conventional method may sometimes cause severe delays while displaying objects. In order to ease this problem, we propose a method where all photographic images are stored into multiple video files, extracted in the memory at startup, and processed in parallel by the graphics processing unit (GPU) to save the time required for seeking and decoding video files.
Neurotransmitter diversity in pre‐synaptic terminals located in the parvicellular neuroendocrine paraventricular nucleus of the rat and mouse hypothalamus

Virtually all rodent neuroendocrine corticotropin‐releasing‐hormone (CRH) neurons are in the dorsal medial parvicellular (mpd) part of the paraventricular nucleus of the hypothalamus (PVH). They form the final common pathway for adrenocortical stress responses. Their activity is controlled by sets of GABA‐, glutamate‐, and catecholamine‐containing inputs arranged in an interactive pre‐motor network. Defining the nature and arrangement of these inputs can help clarify how stressor type and intensity information is conveyed to neuroendocrine neurons. Here we use immunohistochemistry with high‐resolution 3‐dimensional image analyses to examine the arrangement of single‐ and co‐occurring GABA, glutamate, and catecholamine markers in synaptophysin‐defined pre‐synaptic terminals in the PVHmpd of unstressed rats and Crh‐IRES‐Cre;Ai14 transgenic mice: respectively, vesicular glutamate transporter 2 (VGluT2), vesicular GABA transporter (VGAT), dopamine β‐hydroxylase (DBH), and phenylethanolamine n‐methyltransferase (PNMT). Just over half of all PVHmpd pre‐synaptic terminals contain VGAT, with slightly less containing VGluT2. The vast majority of terminal appositions with mouse CRH neurons occur non‐somatically. However, there are significantly more somatic VGAT than VGluT2 appositions. In the rat PVHmpd, about five times as many pre‐synaptic terminals contain PNMT than DBH only. However, because epinephrine release has never been detected in the PVH, PNMT terminals may functionally be noradrenergic not adrenergic. PNMT and VGluT2 co‐occur in some pre‐synaptic terminals indicating the potential for co‐transmission of glutamate and norepinephrine. Collectively, these results provide a structural basis for how GABA/glutamate/catecholamine interactions enable adrenocortical responses to fast‐onset interosensory stimuli, and more broadly, how combinations of PVH neurotransmitters and neuromodulators interact dynamically to control adrenocortical activity.
Emergence of Carbapenem Non-susceptible Campylobacter coli after Long-term Treatment against Recurrent Bacteremia in a Patient with X-linked Agammaglobulinemia

We herein report a case of recurrent Campylobacter coli bacteremia in a 37-year-old Japanese man with X-linked agammaglobulinemia (XLA). The patient experienced seven episodes of C. coli bacteremia over one year, with an erythematous rash intermittently emerged on the lower limbs. Although hospitalization for intravenous treatment was repeatedly recommended, he obstinately declined it. Following long-term oral antibiotic treatment with tebipenem and faropenem for the persistent infection, C. coli showed elevated minimum inhibitory concentrations to meropenem, a key drug for severe campylobacteriosis. Physicians should note that the overuse of antibiotics can lead to the emergence of carbapenem-non-susceptible Campylobacter strains.
Anion-Sensitive Fluorophore Identifies the Drosophila Swell-Activated Chloride Channel in a Genome-Wide RNA Interference Screen

When cells swell in hypo-osmotic solutions, chloride-selective ion channels (Clswell) activate to reduce intracellular osmolality and prevent catastrophic cell rupture. Despite intensive efforts to assign a molecular identity to the mammalian Clswell channel, it remains unknown. In an unbiased genome-wide RNA interference (RNAi) screen of Drosophila cells stably expressing an anion-sensitive fluorescent indicator, we identify Bestrophin 1 (dBest1) as the Drosophila Clswell channel. Of the 23 screen hits with mammalian homologs and predicted transmembrane domains, only RNAi specifically targeting dBest1 eliminated the Clswell current (IClswell). We further demonstrate the essential contribution of dBest1 to Drosophila IClswell with the introduction of a human Bestrophin disease-associated mutation (W94C). Overexpression of the W94C construct in Drosophila cells significantly reduced the endogenous IClswell. We confirm that exogenous expression of dBest1 alone in human embryonic kidney (HEK293) cells creates a clearly identifiable Drosophila–like IClswell. In contrast, activation of mouse Bestrophin 2 (mBest2), the closest mammalian ortholog of dBest1, is swell-insensitive. The first 64 residues of dBest1 conferred swell activation to mBest2. The chimera, however, maintains mBest2-like pore properties, strongly indicating that the Bestrophin protein forms the Clswell channel itself rather than functioning as an essential auxiliary subunit. dBest1 is an anion channel clearly responsive to swell; this activation depends upon its N-terminus.
Minimal area test points for deterministic patterns

Conflict-aware test points, introduced recently, facilitate significant reductions in deterministic test pattern counts. However, dedicated flip-flops driving control points increase test logic area. This paper presents a method to minimize silicon area needed to implement conflict-aware test points by reusing functional flip-flops as drivers of control points. Conflict analysis is applied during the test point selection process, and ATPG verification is run for every potential candidate. Experimental results show that functional flip-flops can be reused as drivers for more than 90% of the control points with the average of 5% penalty in pattern count increase as compared to methods using only dedicated flip-flops. After replacing dedicated flip-flops with functional flip-flops, conflict-aware test points can still achieve remarkable pattern count reductions.
Newtonized Orthogonal Matching Pursuit for Line Spectrum Estimation with Multiple Measurement Vectors

A Newtonized orthogonal matching pursuit (NOMP) algorithm is proposed to estimate continuous frequencies and amplitudes of a mixture of sinusoids with multiple measurement vectors (MMVs). The proposed algorithm includes two key steps: Detecting a new sinusoid on an oversampled discrete Fourier transform (DFT) grid and refining the parameters of already detected sinusoids to avoid the problem of basis mismatch. We provide a stopping criterion based on the overestimating probability of the model order. In addition, the convergence of the proposed algorithm is also proved. Finally, numerical results are conducted to investigate the effectiveness of the proposed algorithm when compared against the state-of-the-art algorithms in terms of frequency estimation accuracy and run time.
Analysis of Maceaene and Macamide Contents of Petroleum Ether Extract of Black, Yellow, and Purple Lepidium Meyenii (Maca) and Their Antioxidant Effect on Diabetes Mellitus Rat Model

Maceaene and macamide contents as well as antioxidant effect of petroleum ether extract of black maca (BM), yellow maca (YM), and purple maca (PM) on diabetes mellitus (DM) rats were investigated. The results showed that seven, six, and five analogues of macamides were identified from the petroleum ether extracts of BM, YM, and PM, respectively. BM extract exhibited the highest contents of total macamides. Comparatively, the PM extract has the lowest macamide quantity. The maceaene contents in all the extracts showed no significant difference (p>0.05). Macamide contents in maca with the same color were not statistically different. Pharmacological results showed that 60-day oral administration of the petroleum ether extract of maca (100 mg/kg.d) can significantly decrease lipid oxidation as indicated by the decreased thiobarbituric acid reactive substances (TBARS) and carbonylated proteins (CP) concentrations on DM rat model (P<0.05). Among them, oral administration of PM extract showed the lowest TBRAS and CP concentrations. All maca extracts can enhance antioxidant enzyme (SOD, superoxide dismutase; CAT, catalase) activity of liver and red blood cells (RBC) of DM rat. However, only oral administration of PM extract can increase SOD and CAT activity of both RBC and liver. The glutathion (GSH) contents in plasma were significantly increased in DM rats treated with PM extract (p<0.05). But, oral administration of BM and YM extracts did not enhance GSH levels. Take together, the data suggested that PM extract exhibited the most potent antioxidant activity on DM rat model. And, maceaene and macamide in maca extract was not correlated with its antioxidant ability.
FoSSicker: A personalized search engine by location-awareness

With the rapid growth of Web documents collection, achieving high precision at the top retrieved documents has become a major issue for the search engine users, especially for the different needs of users for the same query. The typical search engines retrieve the same search results to users that cannot satisfy users any more. In this paper, we introduce a location-aware search engine based on machine learning (FoSSicker) to enhance the precision of web search which takes information parsed from IP address as context to personalize the search results. Moreover, we use history (users' clickthrough data) to intelligentize the search engine to top the Web document which is mostly wanted. By experiments, this intelligent search engine is proved to be a faster reactor compared with the existing personalized search engines.
A SYSTEM FOR LARGE-SCALE AUTOMATIC TRAFFIC SIGN RECOGNITION AND MAPPING

We present a system for the large-scale automatic traffic signs recognition and mapping and experimentally justify design choices made for different components of the system. Our system works with more than 140 different classes of traffic signs and does not require labor-intensive labelling of a large amount of training data due to the training on synthetically generated images. We evaluated our system on the large dataset of Russian traffic signs and made this dataset publically available to encourage future comparison.
The travel and residence of spermatozoa in the oviduct of the Gallus domesticus.

Abstract INTRODUCTION THERE is an increasing interest in the rate of travel of spermatozoa along the hen’s oviduct and in their sites of residence. Mimura (1939), after examining the inseminated oviduct microscopically, reported that spermatozoa deposited in the uterus of an empty oviduct reached the infundibulum in 26 minutes. In another paper, Mimura (1941) found that for 2 to 4 hours after intravaginal insemination, spermatozoa had not passed through the uterus. Allen and Grigg (1957), using P32-labeled spermatozoa, reported that 0.07% of spermatozoa inseminated reached the infundibulum in 15 minutes and that 1.3% were found there after 1 hour. Saeki et al. (1963) reported that at 5 hours, 81.5% of the total activity of radioactive spermatozoa was present in the vagina; and at 24 hours, the activity was 23% in the same region. The infundibulum showed 4.8% of the radioactivity at 5 hours; and 58.7% at 24 hours. Residence of spermatozoa…
Association of carotid intima media thickness with atherogenic index of plasma, apo B/apo A-I ratio and paraoxonase activity in patients with non-alcoholic fatty liver disease

Abstract Background: NAFLD patients have higher risk of atherosclerosis cardiovascular disease (ASCVD). apo B/apoA-I ratio and atherogenic index of plasma (AIP) have been suggested as biomarker for ASCVD. Methods: apo A-I, apoB, aryl esterase (ARE) and paraoxonase (PON) activities and carotid intima media thickness (cIMT) were determined in 49 NAFLD patients and 33 controls. Results: Plasma levels of apo A-I, adiponectin, ARE and PON activities decreased in NAFLD patients, while apo B, AIP and apoB/apo A-I ratio level were higher in NAFLD patients compared to controls. Furthermore, cIMT showed a positive association with AIP, apo B/apo A-I ratio and AIP + (apo B/apo A-I) in NAFLD patients. Strikingly, AIP + (apo B/apo A-I) showed a good ability to discriminating increased cIMT in NAFLD patients. Conclusions: The result showed that AIP and apo B/apo A-I associated with cIMT in NAFLD patients; however, more study are needed to prove this concept.
A new description of riboflavin deficiency syndrome in chickens.

Abstract Day-old male broiler chickens were fed for three weeks with diets containing graded levels of riboflavin (0, 0.22, 0.52, 0.88, and 4.53 mg. added per kg. of basal diet). Curled-toe paralysis which is considered indicative of riboflavin deficiency occurred in less than 10% of the birds at the zero levels of added riboflavin while the mortality was about 25%. Commonly, the birds at the lower levels were paralyzed but with their legs spraddled out and without their toes curled downward and inward. The most senstive indicator of riboflavin deficiency was growth rate which was significantly (P
The Temporal Dynamics of Brain Plasticity in Aging

Abstract Cognitive training has been suggested as a possible remediation of decline in brain structure with older age. However, it is unknown whether training effects are transient or enduring, as no studies have examined training-induced plasticity relative to decline in older adults across extended periods with multiple intervention phases. We investigated the temporal dynamics of brain plasticity across periods on and off memory training, hypothesizing that (1) a decline in white matter (WM) microstructure would be observed across the duration of the study and (2) that periods of memory training would moderate the WM microstructural decline. In total, 107 older adults followed a 40-week program, including 2 training periods separated by periods with no intervention. The general decline in WM microstructure observed across the duration of the study was moderated following the training periods, demonstrating that cognitive training may mitigate age-related brain deterioration. The training-related improvements were estimated to subside over time, indicating that continuous training may be a premise for the enduring attenuation of neural decline. Memory improvements were largely maintained after the initial training period, and may thus not rely on continuous training to the same degree as WM microstructure.
Molt induced by dietary zinc in a low-calcium diet.

Three experiments were designed to test the hypothesis that zinc has a specific effect independent of anorexia during induction of molt. In Experiment 1, hens were fed a low-calcium (.08%) basal molt diet to which was added 0, 110, 620, or 1,120 mg/kg (ppm) zinc as zinc sulfate heptahydrate (ZnSO4.7H2O) for 7 days and 0, 1, 400, 2,800, or 4,200 ppm zinc, respectively, for the following 14 days. In Experiment 2, hens were provided ad libitum access to the low-calcium basal molt diet with 2,800 ppm added zinc for 14 days during which a paired control hen received a similar amount of the low-calcium basal molt diet. In Experiment 3, hens were fed the low-calcium basal molt diet on a restricted basis amended with either 0 or 2,800 ppm zinc on a restricted basis for 10 days. In Experiment 1, all hens that consumed zinc had significantly fewer days to last oviposition as compared with control hens, and this occurred without significant differences in body weight or feed consumption for the lowest zinc group. When compared with the control group, higher levels of zinc did decrease body weight and feed consumption. In Experiment 2, the hens consuming the diet with 2,800 ppm zinc (Zn2800) reached last oviposition significantly sooner than control hens, although the Zn2800 hens actually consumed more feed. In Experiment 3, the Zn2800 hens lost more body weight than control hens due partially to earlier reproductive tract regression. Serum luteinizing hormone was increased in the Zn2800 hens. (ABSTRACT TRUNCATED AT 250 WORDS)
Safe Multi-objective Planning with a Posteriori Preferences

Autonomous planning in safety critical systems is a difficult task where decisions must carefully balance optimisation for performance goals of the system while also keeping the system away from safety hazards. These tasks often conflict, and hence present a challenging multi-objective planning problem where at least one of the objectives relates to safety risk. Recasting safety risk into an objective introduces additional requirements on planning algorithms: safety risk cannot be "averaged out" nor can it be combined with other objectives without loss of information and losing its intended purpose as a tool in risk reduction. Thus, existing algorithms for multi-objective planning cannot be used directly as they do not provide any facility to accurately track and update safety risk. A common work around is to restrict available decisions to those guaranteed safe a priori, but this can be overly conservative and hamper performance significantly. In this paper, we propose a planning algorithm based on multiobjective Monte-Carlo Tree Search to resolve these problems by recognising safety risk as a first class objective. Our algorithm explicitly models the safety of the system separately from the performance of the system, uses safety risk to both optimise and provide constraints for safety in the planning process, and uses an ALARP-based preference selection method to choose an appropriate safe plan from its output. The preference selection method chooses from the set of multiple safe plans to weigh risk against performance. We demonstrate the behaviour of the algorithm using an example representative of safety critical decision-making.
Sim-To-Real Optimization Of Complex Real World Mobile Network with Imperfect Information via Deep Reinforcement Learning from Self-play

Mobile network that millions of people use every day is one of the most complex systems in real world. Optimization of mobile network to meet exploding customer demand and reduce CAPEX/OPEX poses greater challenges than in prior works. Learning to solve complex problems in real world to benefit everyone and make the world better has long been ultimate goal of AI. However, it still remains an unsolved problem for deep reinforcement learning (DRL), given imperfect information in real world, huge state/action space, lots of data needed for training, associated time/cost, multi-agent interactions, potential negative impact to real world, etc. To bridge this reality gap, we proposed a DRL framework to direct transfer optimal policy learned from multi-tasks in source domain to unseen similar tasks in target domain without any further training in both domains. First, we distilled temporal-spatial relationships between cells and mobile users to scalable 3D image-like tensor to best characterize partially observed mobile network. Second, inspired by AlphaGo, we used a novel self-play mechanism to empower DRL agent to gradually improve its intelligence by competing for best record on multiple tasks. Third, a decentralized DRL method is proposed to coordinate multi-agents to compete and cooperate as a team to maximize global reward and minimize potential negative impact. Using 7693 unseen test tasks over 160 unseen simulated mobile networks and 6 field trials over 4 commercial mobile networks in real world, we demonstrated the capability of our approach to direct transfer the learning from one simulator to another simulator, and from simulation to real world. This is the first time that a DRL agent successfully transfers its learning directly from simulation to very complex real world problems with incomplete and imperfect information, huge state/action space and multi-agent interactions.
Prediction-Based Event Determination in Underwater Wireless Sensor Networks

Underwater environments may vary gradually even when the occurrence of events is detected. Sensory data may follow a certain trend and are predictable during certain time durations. Taken these into concerns, a prediction mechanism can be adopted for estimate, and data are synchronized by underwater sensor nodes only when variation is beyond pre-specified thresholds. Leveraging predicted data, the coverage and sources of potential events are identified by the sink node, and the evolution of these events is determined accordingly. Evaluation results show the applicability and energy-efficiency of this approach, especially when the variation of network environments follows certain and simple patterns.
Care coordination between specialty care and primary care: a focus group study of provider perspectives on strong practices and improvement opportunities

Care coordination between the specialty care provider (SCP) and the primary care provider (PCP) is a critical component of safe, efficient, and patient-centered care. Veterans Health Administration conducted a series of focus groups of providers, from specialty care and primary care clinics at VA Medical Centers nationally, to assess 1) what SCPs and PCPs perceive to be current practices that enable or hinder effective care coordination with one another and 2) how these perceptions differ between the two groups of providers. A qualitative thematic analysis of the gathered data validates previous studies that identify communication as being an important enabler of coordination, and uncovers relationship building between specialty care and primary care (particularly through both formal and informal relationship-building opportunities such as collaborative seminars and shared lunch space, respectively) to be the most notable facilitator of effective communication between the two sides. Results from this study suggest concrete next steps that medical facilities can take to improve care coordination, using as their basis the mutual understanding and respect developed between SCPs and PCPs through relationship-building efforts.
Lipschitz-Margin Training: Scalable Certification of Perturbation Invariance for Deep Neural Networks

High sensitivity of neural networks against malicious perturbations on inputs causes security concerns. To take a steady step towards robust classifiers, we aim to create neural network models provably defended from perturbations. Prior certification work requires strong assumptions on network structures and massive computational costs, and thus the range of their applications was limited. From the relationship between the Lipschitz constants and prediction margins, we present a computationally efficient calculation technique to lower-bound the size of adversarial perturbations that can deceive networks, and that is widely applicable to various complicated networks. Moreover, we propose an efficient training procedure that robustifies networks and significantly improves the provably guarded areas around data points. In experimental evaluations, our method showed its ability to provide a non-trivial guarantee and enhance robustness for even large networks.