Miracle-dz/UniFAR-FTUs huggingface dataset:
mTM-align: a server for fast protein structure database search and multiple protein structure alignment

Abstract With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2–5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai. edu.cn/mTM-align/.
From low to high pathogenicity—Characterization of H7N7 avian influenza viruses in two epidemiologically linked outbreaks

The ability of low pathogenic (LP) avian influenza viruses (AIV) of the subtypes H5 and H7 to mutate spontaneously to highly pathogenic (HP) variants is the main reason for their stringent control. On-the-spot evidence from the field of mutations in LPAIV to render the virus into nascent HP variants is scarce. Epidemiological investigations and molecular characterization of two spatiotemporally linked outbreaks caused by LP, and subsequently, HPAIV H7N7 in two-layer farms in Germany yielded such evidence. The outbreaks occurred within 45 days on farms 400 m apart. The LP progenitor virus was identified on both farms, with its putative HP inheritor cocirculating and then dominating on the second farm. As postulated before, mutations in the hemagglutinin cleavage site (HACS) proved to be the most decisive change in the genome of HPAIV, in this case, it was mutated from monobasic (LP) PEIPKGR*GLF into polybasic (HP) PEIPKRKRR*GLF. The full-length genome sequences of both viruses were nearly identical with only ten coding mutations outside the HACS scattered along six genome segments in the HPAIV. Five of these were already present as minor variants in the LPAIV quasispecies of the LPAI-only affected farm. H7-specific seroconversion of part of the chicken population together with the codetection of LPAIV HACS sequences in swab samples of the HPAI outbreak farm suggested an initial introduction of the LP progenitor and a subsequent switch to HPAIV H7N7 after the incursion. The findings provide rare field evidence for a shift in pathogenicity of a notifiable AIV infection and re-inforce the validity of current approaches of control measures to curtail low pathogenic H5 and H7 virus circulation in poultry.
Carcass and meat quality of dual‐purpose chickens (Lohmann Dual, Belgian Malines, Schweizerhuhn) in comparison to broiler and layer chicken types

ABSTRACT Currently, there is an intensive ethical discussion about the practice of culling day‐old layer cockerels. One solution to avoid this practice could be using dual‐purpose types, where males are fattened for meat and females used for egg production. The aim of the present study was to compare fattening performance, carcass conformation, and composition as well as meat quality of Lohmann Dual, a novel dual‐purpose type, and 2 traditional dual‐purpose types (Belgian Malines and Schweizerhuhn) with 2 broiler types and 1 layer type (Lohmann Brown Plus). Broilers included a conventional line (Ross PM3) and a slower‐growing line (Sasso 51) fulfilling requirements of organic farming. Nine birds of each type were fed on a conventional broiler diet. Feed intake and metabolizability of nitrogen and energy were recorded per pen (n = 3), the latter through excreta sampling. For each bird, carcass conformation was assessed, and weights of body, carcass, breast meat, legs, wings, and inner organs were determined. Additionally, breast angle, an indicator for carcass appeal, and skin color were recorded. Meat quality assessment included determinations of thaw and cooking loss, shear force, meat color, and proximate composition of the breast meat. None of the dual‐purpose types (20 to 30 g ADG) performed as well in growth as the intensively growing broiler line (68 g ADG). However, Lohmann Dual could compete with the slower‐growing broiler line (slower growth but better feed efficiency, similar in carcass weight and breast proportion). Also breast angle was quite similar between Lohmann Dual (100°) and the extensive broiler type (115°C) compared to the intensive broiler line (180°). Meat quality was most favorable in the intensive broilers with the smallest shear force and thawing loss, whereas meat quality was not different between the other types. The Schweizerhuhn performed only at the level of the layer hybrid, and the Belgian Malines was ranked only slightly better.
High‐throughput discovery of functional disordered regions

Partially or fully intrinsically disordered proteins are widespread in eukaryotic proteomes and play important biological functions. With the recognition that well defined protein structure is not a fundamental requirement for function come novel challenges, such as assigning function to disordered regions. In their recent work, Babu and colleagues (Ravarani et al, ) took on this challenge by developing IDR‐Screen, a robust high‐throughput approach for identifying functions of disordered regions.
Decreased expression of Na+-H+ exchanger isoforms 1 and 3 in denervated spontaneously hypertensive rat kidney

ABSTRACT To determine whether the sympathetic nerve plays a role in the regulation of Na+-H+ exchange (NHE) in the kidney of spontaneously hypertensive rats (SHR), we investigated the expression of NHE and NHE regulatory protein family (NHERF) in the denervated kidneys compared with intact kidneys. Twelve-week-old male SHR and age-matched Wistar Kyoto (WKY) rats were used. SHR were randomly assigned to the renal denervated (RDNX, n = 8) or Sham (n = 8) groups. The protein and mRNA expression of NHE1, NHE3, NHERF1 and NHERF2 were assessed in the kidney of the groups. Following the renal denervation, immunohistochemistry and western blot analysis showed that NHE1 and NHE3 protein were signiﬁcantly decreased in the kidney compared with Sham group. NHERF1 protein expression was signiﬁcantly increased in RDNX compared with Sham group, whereas NHERF2 protein expression was signiﬁcantly decreased after renal denervation. Similar results were observed at the mRNA level of NHE1, NHE3, NHERF1 and NHERF2 expression. The present ﬁndings suggest that the renal sympathetic nervous system plays a role in the regulation of NHE1 and NHE3 in the kidney of SHR, and NHERF1 may be involved in the expression of NHE3 in the kidney of SHR.
CLERK is a novel receptor kinase required for sensing of root-active CLE peptides in Arabidopsis

ABSTRACT CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides are secreted endogenous plant ligands that are sensed by receptor kinases (RKs) to convey environmental and developmental inputs. Typically, this involves an RK with narrow ligand specificity that signals together with a more promiscuous co-receptor. For most CLEs, biologically relevant (co-)receptors are unknown. The dimer of the receptor-like protein CLAVATA 2 (CLV2) and the pseudokinase CORYNE (CRN) conditions perception of so-called root-active CLE peptides, the exogenous application of which suppresses root growth by preventing protophloem formation in the meristem. clv2 as well as crn null mutants are resistant to root-active CLE peptides, possibly because CLV2-CRN promotes expression of their cognate receptors. Here, we have identified the CLE-RESISTANT RECEPTOR KINASE (CLERK) gene, which is required for full sensing of root-active CLE peptides in early developing protophloem. CLERK protein can be replaced by its close homologs, SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE (SARK) and NSP-INTERACTING KINASE 1 (NIK1). Yet neither CLERK nor NIK1 ectodomains interact biochemically with described CLE receptor ectodomains. Consistently, CLERK also acts genetically independently of CLV2-CRN. We, thus, have discovered a novel hub for redundant CLE sensing in the root. Highlighted Article: The intricate interplay between CLE-sensing pathways along the spatiotemporal gradient of protophloem formation involves the novel CLE-RESISTANT RECEPTOR KINASE gene.
A New Soft-Switching Topology for Switched Inductor High Gain Boost

This paper proposes a new high-gain soft-switching dc–dc topology based on a switched inductor boost converter (SIBC). A conventional SIBC as a high gain boost topology has the issues of high conduction loss in switching diodes and high switching loss in the main switches. Also, it has severe electromagnetic interference (EMI) issue due to high-frequency ringing formed by parasitic inductance and diode junction capacitors. The new topology is derived with the objective of achieving zero voltage switching (ZVS) turn on of the main switch. Instead of adding extra active clamp zero voltage transition (ZVT) path at the switching node, the proposed topology augments the auxiliary ZVT path to the switching diode path. This is achieved by replacing the switching diodes with synchronous switches. The new topology can achieve soft switching for all the switches and alleviate the EMI issue. All the diodes achieve zero current switching (ZCS) turn off without reverse recovery. Auxiliary switches have ZCS turn on and ZVS turn off, and the main switches have ZVS turn on. The soft-switching SIBC also reduces the conduction loss in the switching diodes. A numerical simulation in PLECS and a prototype hardware are built corresponding to a micro-inverter application with 100 kHz switching frequency. Peak power conversion efficiency of 94.76% is achieved in the hardware prototype with Si devices.
Amalgamation of polyphenols and probiotics induce health promotion

ABSTRACT The residing microbiome with its vast repertoire of genes provide distinctive properties to the host by which they can degrade and utilise nutrients that otherwise pass the gastro-intestinal tract unchanged. The polyphenols in our diet have selective growth promoting effects which is of utmost importance as the state of good health has been linked to dominance of particular microbial genera. The polyphenols in native form might more skilfully exert anti-oxidative and anti-inflammatory properties but in a living system it is the microbial derivatives of polyphenol that play a key role in determining health outcome. This two way interaction has invoked great interest among researchers who have commenced several clinical surveys and numerous studies in in-vitro, simulated environment and living systems to find out in detail about the biomolecules involved in such interaction along with their subsequent physiological benefits. In this review, we have thoroughly discussed these studies to develop a fair idea on how the amalgamation of probiotics and polyphenol has an immense potential as an adjuvant therapeutic for disease prevention as well as treatment.
Physical Activity Recommendations for Health and Beyond in Currently Inactive Populations

Widespread persistent inactivity makes continued efforts in physical activity promotion a persistent challenge. The precise content of physical activity recommendations is not broadly known, and there are concerns that the general messaging of the guidelines, including the recommendations to perform at least 150 min of at least moderate intensity physical activity per week might seem unattainable for and even actually discourage currently inactive people. Here we show that there are a myriad of ways of being physically active, and provide (in part) out-of-the-box examples of evidence based, pragmatic, easily accessible physical activity regimes below 150 min and/or with lower than moderate intensity that yield meaningful health benefits for currently inactive people.
Gossip of Statistical Observations using Orthogonal Polynomials

Consider a network of agents connected by communication links, where each agent holds a real value. The gossip problem consists in estimating the average of the values diffused in the network in a distributed manner. Current techniques for gossiping are designed to deal with worst-case scenarios, which is irrelevant in applications to distributed statistical learning and denoising in sensor networks. We design second-order gossip methods tailor-made for the case where the real values are i.i. d. samples from the same distribution. In some regular network structures, we are able to prove optimality of our methods, and simulations suggest that they are efficient in a wide range of random networks. Our approach of gossip stems from a new acceleration framework using the family of orthogonal polynomials with respect to the spectral measure of the network graph.
Publish/Subscribe Protocol in Wireless Sensor Networks: Improved Reliability and Timeliness

The rapidly-evolving demand of applications using wireless sensor networks in several areas such as building and industrial automation or smart cities, among other, makes it necessary to determine and provide QoS support mechanisms which can satisfy the requirements of applications. In this paper we propose a mechanism that establishes different QoS levels, based on Publish/Subscribe model for wireless networks to meet application requirements, to provide reliable delivery of packet and timeliness. The first level delivers packets in a best effort way. The second one intends to provide reliable packet delivery with a novel approach for Retransmission Timeout (RTO) calculation, which adjusts the RTO depending on the subscriber Packet Delivery Ratio (PDR). The third one provides the same reliable packet delivery as the second one, but in addition, it provides data aggregation trying to be efficient in terms of energy consumption and the use of network bandwidth. The last one provides timeliness in the packet delivery. We evaluate each QoS Level with several performance metrics such as PDR, Message Delivery Ratio, Duplicated and Retransmitted Packet Ratio and Packet Timeliness Ratio to demonstrate that our proposal provides significant improvements based on the increase of the PDR obtained.
Incidence of Musculoskeletal Injury in US Army Unit Types: A Prospective Cohort Study

BACKGROUND: Musculoskeletal injuries during military service are a primary source of disability, resulting in 2.4 million annual health care visits and 25 million limited‐duty days. While the injury incidence during basic training is well documented, there is little understanding of injury distribution by organization type in the US Army following initial training. OBJECTIVE: To compare injury incidence, distribution, and impact across various military units. METHODS: In this prospective observational cohort study, comprehensive injury data from subject questionnaires and medical chart reviews were collected over 12 months for 1430 initially healthy Army personnel, representing combat, combat support, combat service support, and ranger units. Health care utilization and time loss due to injury were also collected. RESULTS: Of 1430 soldiers, 481 (33.6%) had time‐loss injury, 222 (15.5%) were injured without limited work, 60 (4.2%) reported an injury but did not seek medical care, and 667 (46.6%) were uninjured. Across the whole sample, injuries were responsible for 5.9 ± 14.4 medical visits per soldier, 21 902 days of limited work, and $1 337 000 ($1901 ± $6535 per soldier) in medical costs. Considering only those reporting injury, each person averaged 36.3 ± 59.7 limited‐work days. The injury incidence was highest in combat service support units (65.6%), with a risk ratio 1.60 times that of the reference group (combat, 41.1%). CONCLUSION: Combat support and combat service support personnel were more likely to have 1 or more injuries compared to rangers and combat personnel. The higher relative risk of injury in support units should be explored further.
Deep Energy Estimator Networks

Density estimation is a fundamental problem in statistical learning. This problem is especially challenging for complex high-dimensional data due to the curse of dimensionality. A promising solution to this problem is given here in an inference-free hierarchical framework that is built on score matching. We revisit the Bayesian interpretation of the score function and the Parzen score matching, and construct a multilayer perceptron with a scalable objective for learning the energy (i.e. the unnormalized log-density), which is then optimized with stochastic gradient descent. In addition, the resulting deep energy estimator network (DEEN) is designed as products of experts. We present the utility of DEEN in learning the energy, the score function, and in single-step denoising experiments for synthetic and high-dimensional data. We also diagnose stability problems in the direct estimation of the score function that had been observed for denoising autoencoders.
The PL6-Family Plasmids of Haloquadratum Are Virus-Related

Plasmids PL6A and PL6B are both carried by the C23T strain of the square archaeon Haloquadratum walsbyi, and are closely related (76% nucleotide identity), circular, about 6 kb in size, and display the same gene synteny. They are unrelated to other known plasmids and all of the predicted proteins are cryptic in function. Here we describe two additional PL6-related plasmids, pBAJ9-6 and pLT53-7, each carried by distinct isolates of Haloquadratum walsbyi that were recovered from hypersaline waters in Australia. A third PL6-like plasmid, pLTMV-6, was assembled from metavirome data from Lake Tyrell, a salt-lake in Victoria, Australia. Comparison of all five plasmids revealed a distinct plasmid family with strong conservation of gene content and synteny, an average size of 6.2 kb (range 5.8–7.0 kb) and pairwise similarities between 61–79%. One protein (F3) was closely similar to a protein carried by betapleolipoviruses while another (R6) was similar to a predicted AAA-ATPase of His 1 halovirus (His1V_gp16). Plasmid pLT53-7 carried a gene for a FkbM family methyltransferase that was not present in any of the other plasmids. Comparative analysis of all PL6-like plasmids provided better resolution of conserved sequences and coding regions, confirmed the strong link to haloviruses, and showed that their sequences are highly conserved among examples from Haloquadratum isolates and metagenomic data that collectively cover geographically distant locations, indicating that these genetic elements are widespread.
Re-thinking Borders in the Digital Space

On the basis of the arguments advanced by Imad Saleh, Nasreddine Bouhai, and Hakim Hachour (Saleh, Bouhai, & Hachour, 2014) concerning the impact of “digital borders” generated by the Internet on the dynamics of inter-disciplinary research, we have been led to blend disciplines in order to develop the following question: are representations in the digital space located in a borderless communication imagery? Here the humanities are called upon to look into the underpinnings of the meanings assigned to digital space, in its conception and its technological praxis. This question also provokes the following underlying reflections: how could we define the notion of borders in relation to a space that is non-territorialized at the level of human perceptions and where customs officials are not quite “in flesh and blood”? How does a border present itself? Does its representation influence conception and technological praxis? As a matter of priority we define what a border is in space for the purpose of confronting this definition with imagined borders in order to analyze the digital space in its continuum between openness and limits.
Alterations in Morphology and Adult Neurogenesis in the Dentate Gyrus of Patched1 Heterozygous Mice

Many genes controlling neuronal development also regulate adult neurogenesis. We investigated in vivo the effect of Sonic hedgehog (Shh) signaling activation on patterning and neurogenesis of the hippocampus and behavior of Patched1 (Ptch1) heterozygous mice (Ptch1+/−). We demonstrated for the first time, that Ptch1+/− mice exhibit morphological, cellular and molecular alterations in the dentate gyrus (DG), including elongation and reduced width of the DG as well as deregulations at multiple steps during lineage progression from neural stem cells to neurons. By using stage-specific cellular markers, we detected reduction of quiescent stem cells, newborn neurons and astrocytes and accumulation of proliferating intermediate progenitors, indicative of defects in the dynamic transition among neural stages. Phenotypic alterations in Ptch1+/− mice were accompanied by expression changes in Notch pathway downstream components and TLX nuclear receptor, as well as perturbations in inflammatory and synaptic networks and mouse behavior, pointing to complex biological interactions and highlighting cooperation between Shh and Notch signaling in the regulation of neurogenesis.
LiveAdapp : Live adaptive mobile video streaming during large scale events

Live uploading video streams are becoming increasingly popular with the recent release of Facebook Live and Periscope. Whereas adaptive live streaming is the standard for video delivery, this technology is not used in sending live video streams from smartphones. Current live streaming apps provide one video quality and are not able to provide stable video streams in bad networking conditions, when many people are streaming at the same time in the same network. Many problems will occur, when all users are competing for available bandwidth. In this paper LiveAdapp is presented which is able to adapt video quality during the capture of a live video stream from smartphones. Several experiments are performed with di↵erent adaptation algorithms in a testbed network, to simulate network conditions in large scale events. By the use of a Smart Network, bandwidth is divided over the number of users in the network. This technology together with a mobile live streaming application which is able to adapt the video quality during live video stream, will provide a stable video stream with the best possible video quality. Besides, bandwidth allocation has an important role regarding problems of competition for available bandwidths among users in the same network. Although, the experiments are not tested in real large audience environments, the results of the simulated networking conditions are promising for future developments.