Miracle-dz/UniFAR-FTUs huggingface dataset:
Rare compound heterozygous variants in PNKP identified by whole exome sequencing in a German patient with ataxia‐oculomotor apraxia 4 and pilocytic astrocytoma

Ataxia-oculomotor apraxia type 4 (AOA4) is a rare autosomal recessive neurologic disorder. The phenotype is characterized by ataxia, oculomotor apraxia, peripheral neuropathy and dystonia. AOA4 is caused by biallelic pathogenic variants in the PNKP gene encoding a polynucleotide kinase 3'-phosphatase with an important function in DNA-damage repair. By whole exome sequencing, we identified 2 variants within the PNKP gene in a 27-year-old German woman with a clinical AOA phenotype combined with a cerebellar pilocytic astrocytoma diagnosed at 23 years of age. One variant, a duplication in exon 14 resulting in the frameshift c. 1253_1269dup p.(Thr424fs*49), has previously been described as pathogenic, for example, in cases of AOA4. The second variant, representing a nonsense mutation in exon 17, c.1545C>G p.(Tyr515*), has not yet been described and is predicted to cause a loss of the 7 C-terminal amino acids. This is the first description of AOA4 in a patient with central European descent. Furthermore, the occurrence of a pilocytic astrocytoma has not been described before in an AOA4 patient. Our data demonstrate compound heterozygous PNKP germline variants in a German patient with AOA4 and provide evidence for a possible link with tumor predisposition. Localization of the 2 variants in human PNKP NP_009185. 2. NM_007254. 3:c. 1253_1269dup p.(Thr424fs*49) is predicted to cause a frameshift within the kinase domain, NM_007254. 3:c.1545C>G p.(Tyr515*) is predicted to cause loss of 2 C-terminal amino acids of the kinase domain and 5 additional C-terminal amino acids.
Neonatal immune challenge followed by adult immune challenge induces epigenetic‐susceptibility to aggravated visceral hypersensitivity

Abdominal pain is one of the major symptoms of inflammatory Bowel Disease (IBD). The inflammatory mediators released by colon inflammation are known to sensitize the afferent neurons, which is one of the contributors to abdominal pain. However, not all IBD patients have abdominal pain, and some patients report abdominal pain during remission, suggesting contributions of other pathological factors to abdominal pain in IBD. Epidemiological studies found early‐life gastrointestinal infections a risk factor for IBD symptoms and adult‐life gastrointestinal infections may trigger the onset of IBD. We investigated the hypothesis that neonatal colon immune challenge followed by an adult colon immune challenge upregulates spinal cord BDNF that aggravates visceral sensitivity over and above that induced by adult colon immune challenge alone.
Frontiers inEcology and the Environment Maximizing arthropod-mediated ecosystem services in agricultural landscapes : the role of native plants

R Ru uf fu us s I Is sa aa ac cs s, , J Ju ul li ia an nn na a T Tu ue el ll l, , A An nn na a F Fi ie ed dl le er r, , M Ma ar ry y G Ga ar rd di in ne er r, , a an nd d D Do ou ug g L La an nd di is s This article is citable (as shown above) and is released from embargo once it is posted to the Frontiers e-View site (www.frontiersinecology.org). Please note: This article was downloaded from Frontiers e-View, a service that publishes fully edited and formatted manuscripts before they appear in print in Frontiers in Ecology and the Environment. Readers are strongly advised to check the final print version in case any changes have been made.
A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

MOTIVATION High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome-genome comparisons. RESULTS We introduce a new algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every position of the text, a sparse SA occupies much less memory. Even though we use a sparse index, the output of our algorithm is the same as a full text index algorithm as long as the space between the indexed suffixes is not greater than a minimum length of a MEM. By relying on partial matches and additional text scanning between indexed positions, the algorithm trades memory for extra computation. The reduced memory usage makes it possible to determine MEMs between significantly longer sequences. AVAILABILITY Source code for the algorithm is available under a BSD open source license at http://compbio.cs. princeton.edu/mems. The implementation can serve as a drop-in replacement for the MEMs algorithm in MUMmer 3.
Use of the Short Physical Performance Battery Score to predict loss of ability to walk 400 meters: analysis from the InCHIANTI study.

BACKGROUND Early detection of mobility limitations remains an important goal for preventing mobility disability. The purpose of this study was to examine the association between the Short Physical Performance Battery (SPPB) and the loss of ability to walk 400 m, an objectively assessed mobility outcome increasingly used in clinical trials. METHODS The study sample consisted of 542 adults from the InCHIANTI study aged 65 and older, who completed the 400 m walk at baseline and had evaluations on the SPPB and 400 m walk at baseline and 3-year follow-up. Multiple logistic regression models were used to determine whether SPPB scores predict the loss of ability to walk 400 m at follow-up among persons able to walk 400 m at baseline. RESULTS The 3-year incidence of failing the 400 m walk was 15.5%. After adjusting for age, sex, education, body mass index, Mini-Mental State Examination, number of medical conditions, and 400 m walk gait speed at baseline, SPPB score was significantly associated with loss of ability to walk 400 m after 3 years. Participants with SPPB scores of 10 or lower at baseline had significantly higher odds of mobility disability at follow-up (odds ratio [OR] = 3.38, 95% confidence interval [CI]: 1.32-8.65) compared with those who scored 12, with a graded response across the range of SPPB scores (OR = 26.93, 95% CI: 7.51-96.50; OR = 7.67, 95% CI: 2.26-26.04; OR = 8.28, 95% CI: 3.32-20.67 for SPPB < or = 7, SPPB 8, and SPPB 9, respectively). CONCLUSIONS The SPPB strongly predicts loss of ability to walk 400 m. Thus, using the SPPB to identify older persons at high risk of lower body functional limitations seems a valid means of recognizing individuals who would benefit most from preventive interventions.
SUDMAD: Sequential and unsupervised decomposition of a multi‐author document based on a hidden markov model

Decomposing a document written by more than one author into sentences based on authorship is of great significance due to the increasing demand for plagiarism detection, forensic analysis, civil law (i.e., disputed copyright issues), and intelligence issues that involve disputed anonymous documents. Among existing studies for document decomposition, some were limited by specific languages, according to topics or restricted to a document of two authors, and their accuracies have big room for improvement. In this paper, we consider the contextual correlation hidden among sentences and propose an algorithm for Sequential and Unsupervised Decomposition of a Multi‐Author Document (SUDMAD) written in any language, disregarding topics, through the construction of a Hidden Markov Model (HMM) reflecting the authors' writing styles. To build and learn such a model, an unsupervised, statistical approach is first proposed to estimate the initial values of HMM parameters of a preliminary model, which does not require the availability of any information of author's or document's context other than how many authors contributed to writing the document. To further boost the performance of this approach, a boosted HMM learning procedure is proposed next, where the initial classification results are used to create labeled training data to learn a more accurate HMM. Moreover, the contextual relationship among sentences is further utilized to refine the classification results. Our proposed approach is empirically evaluated on three benchmark datasets that are widely used for authorship analysis of documents. Comparisons with recent state‐of‐the‐art approaches are also presented to demonstrate the significance of our new ideas and the superior performance of our approach.
Enabling the Development and Deployment of Next Generation Point-of-Care Diagnostics

A major goal of the 1st International Point-of-Care Diagnostic Workshop in Nairobi, Kenya was to provide a forum for open dialog concerning current challenges in, and potential solutions for, the development of the next generation of POC diagnostics. The focus was not solely on descriptions of new technologies in development but also included demonstrations of their use in a field setting. The resulting conversations identified a number of obstacles to the successful translation of prototypes into field-deployable tools. These obstacles superseded those typically encountered in research; changes must be implemented at the institutional and governmental level to enable equitable collaborations between Western and African partners, and proper funding mechanisms must be established to support these collaborations. Additionally, this workshop showcased emerging technologies for POC tests and fostered new partnerships between technology developers and African research laboratories. Equitable partnerships are critical for the successful implementation of new POC technology. The attendees agreed that the most effective methods to effect change require improved communication of needs, ideas and abilities, and a conduit for the sharing of experiences and information. We plan to implement many of the changes that are suggested here in our own research programs and to use future conferences and workshops to guide the development of both technologies and partnerships. Our successes and failures will serve as models for those scientists striving to develop technological and biomedical solutions to similar problems in global health.
Metabolites in stored platelets associated with platelet recoveries and survivals

Transfusion of platelets (PLTs) is a common therapy in a number of clinical settings. However, it is well understood that there is substantial donor‐to‐donor variation in how well PLTs store and thus the quality of the products that are transfused. The basis of such variation is poorly understood, and there are limited metrics by which units of PLTs can be assessed for their posttransfusion performance. It has repeatedly been demonstrated that myriad biologic changes take place during PLT storage; however, which of the changes correlate with quality of the stored PLTs and/or are mechanistically involved in PLT function remains undetermined.
Epigenetic Status of H19-Igf2 Imprinted Genes and Loss of 5-Hydroxymethylcytosine in the Brain of Cloned Goats.

In mammals, the imprinted genes play vital roles in development and are generally controlled by DNA methylation at imprinting control regions (ICRs). Recently, it was discovered that 5-hydroxymethylcytosine (5-hmC) is a stable epigenetic modification; however, its functions in cloned animal genomes have not yet been fully elucidated. In this study, we interrogated and quantified the 5-hmC levels in the brain of cloned goats and discovered upregulation of Uhrf1 (p < 0.001), Dnmt1 (p < 0.05), Dnmt3a (p < 0.05), Igf2 (p < 0.01), and H19 (p < 0.05) and downregulation of Dnmt3b (p < 0.001), Tet1 (p < 0.001), Tet2 (p < 0.05), Tet3 (p < 0.001), Mecp2 (p < 0.05), and Igf2r (p < 0.05) in deceased cloned goat tissues compared with the normal controls. We demonstrated that DNA methylation was increased at H19 ICR (51.33% ± 2.03% vs. 93.07% ± 3.06%; p < 0.01) and that DNA was hypomethylated at Igf2 ICR (4.57% ± 1.48% vs. 7.63% ± 1.83%; p > 0.05) in the brain of deceased cloned goats. Finally, we showed that within the cloned goat brain genome, the amount of genome-wide 5-hmC was significantly decreased (0.083% ± 0.026% vs. 0.024% ± 0.007%; p < 0.05), whereas the 5-hmC levels within H19 and Igf2 CCGG sites were not significantly altered (0.17% ± 0.09% vs. 0.03% ± 0.01%; p > 0.05) in the brain of deceased cloned goats. Our data bring further experimental evidence regarding the abnormalities in 5-hmC and advance our current understanding of the role of 5-hmC in cloned animals.
Influence of time elapsed between application and adhesive polymerization on the bond strength to dentin

The aim of this study was to evaluate the influence of time elapsed between dentin adhesive application and its polymerization on the bond strength to dentin. Superficial bovine dentin received the following treatments: Single Bond (3M/ESPE Dental Products Division, St.Paul, MN, USA), Excite (Ivoclar/Vivadent, Schaan, Liechtenstein), Prime&Bond 2.1 (Dentsply/Caulk, Milford, DE, USA) and One-Up Bond F (Tokuyama Corp.,Tokyo, Japan) being polymerized immediately after its application, 10 and 20 seconds after application. After, indirect composite restoration was fixed with resinous cement RelyX Arc (3M/ESPE). The restoration/tooth interface was observed on Scanning Electron Microscopy (SEM). Bond strength was accessed through a shear bond test on a testing machine at 0.5 mm/min. Data were compared by ANOVA followed by Tukey test (α =0.05). The failure modes was observed by means of stereo-microscope (40X magnification), being classified as adhesive, dentin cohesive, resin cohesive and mixed failure. There was no significant difference on the bond strength between the 10s and 20s groups for the majority of the materials. However, both the failure modes and the SEM showed better interaction between dentin and adhesive systems after elapsed 20s its application. It was concluded that longer periods of adhesive system application resulted on better interaction between dentin and adhesive systems evaluated.
Investigation on wear properties of AZ31-MWCNT nanocomposites fabricated through mechanical alloying and powder metallurgy

Abstract The wear properties of Mg alloy AZ31 (Al 3%, Zn 1%, rest Mg) nanocomposites reinforced with multi-wall carbon nanotubes (MWCNTs) were studied by conducting experiments on pin-on-disc wear test apparatus. The composites were fabricated by powder metallurgy technique by homogeneously reinforcing variable percentages of MWCNTs (0.33 wt%, 0.66 wt%, and 1.0 wt%) into Mg alloy AZ31 matrix through mechanical alloying. The effect of varying percentages of MWCNTs on the wear properties of AZ31-MWCNT nanocomposites and the mechanism behind that were investigated through scanning electron microscope and energy dispersive spectroscope analysis. The microstructure investigation revealed that an increase in reinforcement of MWCNTs in AZ31 alloy increased the hardness and reduced the wear rate of the composites with 0.33 wt% and 0.66 wt% due to homogeneous distribution and high interfacial strength between AZ31 and MWCNTs. However, with the addition of 1.0 wt% MWCNTs to AZ31 alloy led to high agglomeration of MWCNTs, resulting in poor interfacial strength and weak bonding between AZ31 and conglomerated MWCNTs, subsequently increasing the wear rate.
Fair and Diverse DPP-based Data Summarization

Sampling methods that choose a subset of the data proportional to its diversity in the feature space are popular for data summarization. However, recent studies have noted the occurrence of bias (under- or over-representation of a certain gender or race) in such data summarization methods. In this paper we initiate a study of the problem of outputting a diverse and fair summary of a given dataset. We work with a well-studied determinantal measure of diversity and corresponding distributions (DPPs) and present a framework that allows us to incorporate a general class of fairness constraints into such distributions. Coming up with efficient algorithms to sample from these constrained determinantal distributions, however, suffers from a complexity barrier and we present a fast sampler that is provably good when the input vectors satisfy a natural property. Our experimental results on a real-world and an image dataset show that the diversity of the samples produced by adding fairness constraints is not too far from the unconstrained case, and we also provide a theoretical explanation of it.
The effects of adrenocorticotropic hormone and heat stress on the distribution of lymphocyte populations in immature male chickens.

This study investigated the effects of heat stress and adrenocorticotropic hormone (ACTH) on the distribution of lymphocyte populations. Two experiments were conducted; each used 12-wk-old Cornell K-strain male chickens. In Experiment 1, birds were exposed to a temperature of 35 C, 6 h/d for 5 d and control birds were maintained at 24 C. In Experiment 2, birds received daily i.m. injections of 50 IU/kg body weight of ACTH for 5 d and control birds received . 9% saline. On Day 6, blood and spleens were collected and lymphocytes were isolated. Indirect immunofluorescent labeling of lymphocytes were performed to detect B lymphocytes, CD4+ cells, and CD8+ cells. Neither ACTH injection nor heat stress affected percentages of B lymphocytes in the blood or the spleen. The CD4+ cells decreased significantly in the blood of ACTH-injected and heat-stressed birds and significantly increased in the spleens of heat-stressed birds. The CD4+ cells in the spleens of ACTH-injected birds did not differ from controls. The CD8+ cells significantly declined in the blood following both ACTH injection and heat stress and significantly increased in the spleen of the ACTH-injected birds but did not differ from controls in the heat-stressed birds. These results indicate that stress factors lead to redistribution of different lymphocyte populations.
Enabling drone as a service: OneM2M-based UAV/drone management system

Recently, commercial Unmanned Aerial Vehicles (UAVs) called drones have received a lot of interest in the public and civil environments for their possibility as a potential enabler of promising services such as traffic monitoring, ad hoc network establishment in a disaster area, parcel delivery, remote sensing and streaming on various service scenarios. However, in order to support those services smoothly, a stable and reliable UAV/drone control and management system is needed. Utilizing a standard-based communication scheme is helpful in realizing efficient control and management of UAV/drone-based operations. Regarding this issue, the oneM2M global standard, which provides machine-to-machine (M2M) and the Internet of Things (IoT) service layer for globally interoperable M2M/IoT solutions, has paramount benefit. In this paper, we present oneM2M global standard platform based UAV/drone management system based on the Interworking Proxy Entity (IPE) for drones. We also show our implementation and demonstration for the oneM2M based UAV/drone management system.
Energy and protein relationships in the broiler. 1. Effect of protein levels and feeding regimens on growth, body composition, and in vitro lipogenesis of broiler chicks.

Male broiler chicks were fed ad libitum diets containing 18, 23, or 30% protein for 3 weeks. In addition, chicks were fed diets containing 12, 23, or 30% protein on a 3-day rotation. Finally, chicks were fed either the 23 or 30% protein on a schedule of 2 days on feed and 1 day off feed. These feeding schemes allowed chicks to consume low to excess protein coupled with either adequate or inadequate energy intake. Feed intakes were equal for the 18, 23, and rotational percent protein dietary groups and lower (P less than .05) for the 30% ad libitum group. Chicks fed the 18% protein diet ad libitum were the least efficient (P less than .05) at utilizing feed and the most efficient (P less than .05) at utilizing protein for weight gain. Compared to the ad libitum situation, restricted feeding improved feed and protein efficiency of chicks fed 30% protein diets but not of chicks fed 23% protein diets. Body composition data on a dry matter basis supported a positive relationship between dietary protein and percent lean tissue. Conversely, expressing data on a whole bird basis indicated that lean body mass was favored by feeding the diet containing 23% protein. In vitro lipogenesis was greatest (P less than .05) in chicks fed a 18% protein diet ad libitum and least (P less than .05) in chicks fed a 30% protein diets ad libitum. (ABSTRACT TRUNCATED AT 250 WORDS)
Are wearable EEG devices more accurate than fitness wristbands for home sleep Tracking? Comparison of consumer sleep trackers with clinical devices

This study aimed to compare two off-the-shelf sleep tracking devices, Fitbit (wearable fitness wristband) and Neuroon (wearable EEG eye mask), for measuring sleep under free living conditions. Taking the measurements of a clinical sleep monitor as the ground truth, we compared the measurements of Fitbit and Neuroon on total sleep time (TST), wake after sleep onset (WASO), the number of awakenings (NAWK), sleep onset latency (SOL), and sleep efficiency (SE). Although the users of home sleep tracking technologies generally assume that the measurements by EEG-based sleep trackers are more accurate than movement-based wristbands, our study showed that compared to Neuroon EEG eye mask, the measurements by Fitbit wristband agreed better to those of the clinical device.
Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis

Since 1967, Rifampin (RMP, a Rifamycin) has been used as a first line antibiotic treatment for tuberculosis (TB), and it remains the cornerstone of current short‐term TB treatment. Increased occurrence of Rifamycin‐resistant (RIFR) TB, ∼41% of which results from the RpoB S531L mutation in RNA polymerase (RNAP), has become a growing problem worldwide. In this study, we determined the X‐ray crystal structures of the Escherichia coli RNAPs containing the most clinically important S531L mutation and two other frequently observed RIFR mutants, RpoB D516V and RpoB H526Y. The structures reveal that the S531L mutation imparts subtle if any structural or functional impact on RNAP in the absence of RIF. However, upon RMP binding, the S531L mutant exhibits a disordering of the RIF binding interface, which effectively reduces the RMP affinity. In contrast, the H526Y mutation reshapes the RIF binding pocket, generating significant steric conflicts that essentially prevent any RIF binding. While the D516V mutant does not exhibit any such gross structural changes, certainly the electrostatic surface of the RIF binding pocket is dramatically changed, likely resulting in the decreased affinity for RIFs. Analysis of interactions of RMP with three common RIFR mutant RNAPs suggests that modifications to RMP may recover its efficacy against RIFR TB.