Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved efficiency for explicit covering codes matching the sphere-covering bound

A covering code is a subset of vectors over a finite field with the property that any vector in the space is close to some codeword in Hamming distance. Blinovsky [Bli90] showed that most linear codes have covering radius attaining the sphere-covering bound. Taking the direct sum of all $2^{O(n^2)}$ linear codes gives an explicit code with optimal covering density, which is, to our knowledge, the most efficient construction. In this paper, we improve the randomness efficiency of this construction by proving optimal covering property of a Wozencraft-type ensemble. This allows us to take the direct sum of only $2^{O(n\log n)}$ many codes to achieve the same covering goodness. The proof is an application of second moment method coupled with an iterative random shift trick along the lines of Blinovsky.
Spatially Structured Environmental Variation Plays a Prominent Role on the Biodiversity of Freshwater Macrophytes Across China

Different non-mutually exclusive mechanisms interactively shape large-scale diversity patterns. However, our understanding of multi-faceted diversity and their determinants in aquatic ecosystems is far from complete compared to terrestrial ones. Here, we use variation partitioning based on redundancy analysis to analyze the relative contribution of environmental and spatial variables to the patterns of phylogenetic, taxonomic, and functional diversity in macrophyte assemblages across 214 Chinese watersheds. We found extremely high spatial congruence among most aspects of biodiversity, with some important exceptions. We then used variation partitioning to estimate the proportions of variation in macrophyte biodiversity explained by environmental and spatial variables. All diversity facets were optimally explained by spatially structured environmental variables, not the pure environment effect, implying that macrophyte are taxonomically, phylogenetically, and functionally clustered in space, which might be the result of the interaction of environmental and/or evolutionary drives. We demonstrate that macrophytes might face extensive dispersal limitations across watersheds such as topography and habitat fragmentation and availability.
Phenylboronic acid-modified hollow silica nanoparticles for dual-responsive delivery of doxorubicin for targeted tumor therapy

Abstract This work reports a multifunctional nanocarrier based on hollow mesoporous silica nanoparticles (HMSNs) for targeting tumor therapy. Doxorubicin (DOX) was loaded into HMSNs and blocked with cytochrome C conjugated lactobionic acid (CytC–LA) via redox-cleavable disulfide bonds and pH-disassociation boronate ester bonds as intermediate linkers. The CytC–LA was used both as sealing agent and targeting motif. A series of characterizations demonstrated the successful construction of the drug delivery system. The system demonstrated pH and redox dual-responsive drug release behavior in vitro. The DOX loading HMSNs system displayed a good biocompatibility, which could be specifically endocytosed by HepG2 cells and led to high cytotoxicity against tumor cells by inducing cell apoptosis. In vivo data (tumor volume, tumor weight, terminal deoxynucleotidyl transferase dUTP nick end labeling and hematoxylin and eosin staining) proved that the system could deliver DOX to tumor site with high efficiency and inhibit tumor growth with minimal toxic side effect.
Inflammatory Cytokine Networks in Gastrointestinal Tract Graft vs. Host Disease

Graft vs. host disease (GVHD) is the major non-relapse complication associated with allogeneic hematopoietic stem cell transplantation (HSCT). Damage to the gastrointestinal (GI) tract from acute GVHD is a particularly serious event that can result in significant morbidity and mortality. Proinflammatory cytokines play a critical role in the pathophysiology of intestinal GVHD, in part by activating donor T cell populations which subsequently induce tissue damage. In this review, we summarize pre-clinical data derived from experimental murine models that have examined the role of inflammatory cytokine pathways that play critical roles in the pathophysiology of GVHD of the GI tract. Specific areas of focus are on STAT 3-dependent cytokines (e.g., IL-6, IL-23, and IL-21), and members of the IL-1 cytokine family, both of which have been shown to induce pathological damage within the GI tract during this disease. We also review established and ongoing efforts to translate these pre-clinical findings into the clinic in an effort to reduce morbidity and mortality due to this complication.
Evaluation of DNA Extraction Methods on Individual Helminth Egg and Larval Stages for Whole-Genome Sequencing

Whole genome sequencing is being rapidly applied to the study of helminth genomes, including de novo genome assembly, population genetics, and diagnostic applications. Although late-stage juvenile and adult parasites typically produce sufficient DNA for molecular analyses, these parasitic stages are almost always inaccessible in the live host; immature life stages found in the environment for which samples can be collected non-invasively offer a potential alternative, however, these samples are typically yield very low quantities of DNA, can be environmentally resistant, and are susceptible to contamination, often from bacterial or host DNA. Here, we have tested five low-input DNA extraction protocols together with a low-input sequencing library protocol to assess the feasibility of whole genome sequencing of individual immature helminth samples. These approaches do not use whole genome amplification, a common but costly approach to increase the yield of low input samples. We first tested individual parasites from two species spotted onto FTA cards - egg and L1 stages of Haemonchus contortus and miracidia of Schistosoma mansoni - before further testing on an additional six species - Ancylostoma caninum, Ascaridia dissimilis, Dirofilaria immitis, Dracunculus medinensis, Strongyloides stercoralis, and Trichuris muris - with an optimal protocol. Whole genome sequencing followed by analyses to determine the proportion of on- and off-target mapping revealed successful sample preparations for six of the eight species tested with variation between species, and within species but between life stages, described. These results demonstrate the feasibility of whole genome sequencing of individual parasites, and highlight a new avenue towards generating sensitive, specific, and information-rich data for the diagnosis and surveillance of helminths.
Significance of the Differential Peptidome in Multidrug-Resistant Tuberculosis

Most multidrug-resistant tuberculosis (MDR-TB) patients fail to receive a timely diagnosis and treatment. Therefore, we explored the differentially expressed peptides in MDR-TB compared with drug-susceptible tuberculosis (DS-TB) patients using LC-MS/MS and Ingenuity Pathway Analysis (IPA) to analyse the potential significance of these differentially expressed peptides. A total of 301 peptides were differentially expressed between MDR-TB and DS-TB groups. Of these, 24 and 16 peptides exhibited presented high (fold change ≥ 2.0, P < 0.05) and low (fold change ≤ −2.0, P < 0.05) levels in MDR-TB. Significant canonical pathways included the prothrombin activation system, coagulation system, and complement system. In the network of differentially expressed precursor proteins, lipopolysaccharide (LPS) regulates many precursor proteins, including four proteins correlated with organism survival. These four important differentially expressed proteins are prothrombin (F2), complement receptor type 2 (CR2), collagen alpha-2(V) chain (COL5A2), and inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4). After addition of CR2 peptide, IL-6 mRNA expression in THP-1 cells decreased significantly in dose- and time-dependent manners. Cumulatively, our study proposes potential biomarkers for MDR-TB diagnosis and enables a better understanding of the pathogenesis of MDR-TB. The functions of differentially expressed peptides, especially CR2, in MDR-TB require further investigation.
Mycobacterium riyadhense clinical isolates provide insights into ancestry and adaptive evolution in tuberculosis

Mycobacterium riyadhense is a novel non-tuberculous mycobacterium (NTM) that is increasingly isolated from clinical cases with tuberculosis (TB)-like symptoms in humans in various parts of the world. To elucidate the genomic hallmarks that define the relationship between M. riyadhense and other mycobacterial species, including members of the Mycobacterium tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were analysed. M. riyadhense shares a large number of conserved orthologues with the MTBC and contains linear and circular plasmids carrying type IV and type VII secretion systems. We provide evidence that M. riyadhense is likely the 9missing link9 in the evolution of M. tuberculosis, sharing a common ancestor with members of the MTBC that has evolved through a process of genome reduction, expansion of toxin/antitoxin systems, and ultimately host adaptation. We conclude that M. riyadhense is an emerging mycobacterial pathogen that can serve as an experimental model to study the evolution and pathogenesis of tubercle bacilli.
Streaming of Repeated Noise in Primary and Secondary Fields of Auditory Cortex

Statistical regularities in natural sounds facilitate the perceptual segregation of auditory sources, or streams. Repetition is one cue that drives stream segregation in humans, but the neural basis of this perceptual phenomenon remains unknown. We demonstrated a similar perceptual ability in animals by training ferrets of both sexes to detect a stream of repeating noise samples (foreground) embedded in a stream of random samples (background). During passive listening, we recorded neural activity in primary auditory cortex (A1) and secondary auditory cortex (posterior ectosylvian gyrus, PEG). We used two context-dependent encoding models to test for evidence of streaming of the repeating stimulus. The first was based on average evoked activity per noise sample and the second on the spectro-temporal receptive field. Both approaches tested whether differences in neural responses to repeating versus random stimuli were better modeled by scaling the response to both streams equally (global gain) or by separately scaling the response to the foreground versus background stream (stream-specific gain). Consistent with previous observations of adaptation, we found an overall reduction in global gain when the stimulus began to repeat. However, when we measured stream-specific changes in gain, responses to the foreground were enhanced relative to the background. This enhancement was stronger in PEG than A1. In A1, enhancement was strongest in units with low sparseness (i.e., broad sensory tuning) and with tuning selective for the repeated sample. Enhancement of responses to the foreground relative to the background provides evidence for stream segregation that emerges in A1 and is refined in PEG. SIGNIFICANCE STATEMENT To interact with the world successfully, the brain must parse behaviorally important information from a complex sensory environment. Complex mixtures of sounds often arrive at the ears simultaneously or in close succession, yet they are effortlessly segregated into distinct perceptual sources. This process breaks down in hearing-impaired individuals and speech recognition devices. By identifying the underlying neural mechanisms that facilitate perceptual segregation, we can develop strategies for ameliorating hearing loss and improving speech recognition technology in the presence of background noise. Here, we present evidence to support a hierarchical process, present in primary auditory cortex and refined in secondary auditory cortex, in which sound repetition facilitates segregation.
ComplexFace: a Multi-Representation Approach for Image Classification with Small Dataset

State-of-the-art face recognition algorithms are able to achieve good performance when sufficient training images are provided. Unfortunately, the number of facial images is limited in some real face recognition applications. In this paper, we propose ComplexFace, a novel and effective algorithm for face recognition with limited samples using complex number based data augmentation. The algorithm first generates new representations from original samples and then fuse both into complex numbers, which avoids the difficulty of weight setting in other fusion approaches. A test sample can then be expressed by the linear combination of all the training samples, which mapped the sample to the new representation space for classification by the kernel function. The collaborative representation based classifier is then built to make predictions. Extensive experiments on the Georgia Tech (GT) face database and the ORL face database show that our algorithm significantly outperforms existing methods: the average errors of previous approaches ranging from 31.66% to 41.75% are reduced to 14.54% over the GT database; the average errors of previous approaches ranging from 5.21% to 10.99% are reduced to 1.67% over the ORL database. In other words, our algorithm has decreased the average errors by up to 84.80% on the ORL database.
Over the rainbow: A practical guide for fluorescent protein selection in plant FRET experiments

Receptor-like kinases (RLK) and receptor-like proteins (RLP) often interact in a combinatorial manner depending on tissue identity, membrane domains, or endo- and exogenous cues, and the same RLKs or RLPs can generate different signaling outputs depending on the composition of the receptor complexes they are involved in. Investigation of their interaction partners in a spatial and dynamic way is therefore of prime interest to understand their functions. This is however limited by the technical complexity of assessing it in endogenous conditions. A solution to close this gap is to determine protein interaction directly in the relevant tissues at endogenous expression levels using Förster resonance energy transfer (FRET). The ideal fluorophore pair for FRET must, however, fulfil specific requirements: (i) the emission and excitation spectra of the donor and acceptor, respectively, must overlap; (ii) they should not interfere with proper folding, activity, or localization of the fusion proteins; (iii) they should be sufficiently photostable in plant cells. Furthermore, the donor must yield sufficient photon counts at near-endogenous protein expression levels. Although many fluorescent proteins were reported to be suitable for FRET experiments, only a handful were already described for applications in plants. Herein, we compare a range of fluorophores, assess their usability to study RLK interactions by FRET-based fluorescence lifetime imaging (FLIM) and explore their differences in FRET efficiency. Our analysis will help to select the optimal fluorophore pair for diverse FRET applications. One-sentence summary We compared the performances of several different fluorescent protein pairs to study membrane protein interaction in plants with FRET.
Multi-Player Bandits: The Adversarial Case

We consider a setting where multiple players sequentially choose among a common set of actions (arms). Motivated by a cognitive radio networks application, we assume that players incur a loss upon colliding, and that communication between players is not possible. Existing approaches assume that the system is stationary. Yet this assumption is often violated in practice, e.g., due to signal strength fluctuations. In this work, we design the first Multi-player Bandit algorithm that provably works in arbitrarily changing environments, where the losses of the arms may even be chosen by an adversary. This resolves an open problem posed by Rosenski, Shamir, and Szlak (2016).
Bayesian optimisation under uncertain inputs

Bayesian optimisation (BO) has been a successful approach to optimise functions which are expensive to evaluate and whose observations are noisy. Classical BO algorithms, however, do not account for errors about the location where observations are taken, which is a common issue in problems with physical components. In these cases, the estimation of the actual query location is also subject to uncertainty. In this context, we propose an upper confidence bound (UCB) algorithm for BO problems where both the outcome of a query and the true query location are uncertain. The algorithm employs a Gaussian process model that takes probability distributions as inputs. Theoretical results are provided for both the proposed algorithm and a conventional UCB approach within the uncertain-inputs setting. Finally, we evaluate each method's performance experimentally, comparing them to other input noise aware BO approaches on simulated scenarios involving synthetic and real data.
The Economic Burden and Impact on Quality of Life of Herpes Zoster and Postherpetic Neuralgia in Individuals Aged 50 Years or Older in Italy

Abstract Background To estimate the health care resource utilization, costs, and impact on quality of life (QoL) of herpes zoster (HZ) and postherpetic neuralgia (PHN) in adults aged ≥50 years in Italy. Methods This was a prospective, observational, multicenter, community physician–based surveillance study (NCT01772160) in Italy. Health-related QoL data were collected using the EuroQoL-5 Dimension (EQ-5D) and Zoster Brief Pain Inventory (ZBPI) questionnaires. Both questionnaires were assessed at days 0 (HZ rash onset), 15, 30, 60, and 90 for all patients, and monthly thereafter for patients who developed PHN. Resource utilization was recorded for 3 months post–HZ onset and 9 months for PHN patients. Costs from both payer and societal perspectives were estimated and were composed of direct medical costs (general practitioner/specialist visits, procedures, hospitalizations, medications), work loss by patient/caregiver, and transport costs. Results A total of 391 patients with HZ were included, of whom 40 developed PHN. The mean ZBPI worst pain score was 5.7 at day 0, reducing to 2.6 at day 30 and 0.7 by day 90. Patients with PHN had a mean worst pain score of 5.7 at day 90. We estimated an overall disutility associated with HZ of 0.134. The mean cost per HZ patient from a payer/societal perspective was €153/€298, respectively, and the mean cost per HZ patients who developed PHN was €176/€426, respectively. Conclusions HZ is associated with impaired QoL and substantial health care resource use, highlighting the need for preventive strategies. This could reduce the disease burden for the patient and health care system. ClinicalTrials.gov study registry NCT01772160.
State Filtering for Networked Control Systems Subject to Switching Disturbances

Abstract State estimation of stochastic discrete-time linear systems subject to unknown inputs has been widely studied, but few works take into account disturbances switching between unknown inputs and constant biases. We show that such disturbances affect a networked control system subject to deception attacks on the control signals transmitted by the controller to the plant via unreliable networks. This paper proposes to estimate the switching disturbance from an augmented state version of the intermittent unknown input Kalman filter. The sufficient stochastic stability conditions of the obtained filter are established when the arrival binary sequence of data losses follows a Bernoulli random process.
Plasma Metabolic Characterisation of Dairy Cows with Inactive Ovaries and Oestrus During the Peak of Lactation

Abstract Introduction Differential metabolites (DMs) between cows with inactive ovaries (IO) and oestrous (E) cows were screened and metabolic pathways of DMs associated with IO were determined. Material and Methods Cows at 50 to 60 days (d) postpartum from an intensive dairy farm were randomly selected and allocated into an E group (n = 16) or an IO group (n = 16) according to a pedometer and rectal examinations. Their plasma samples were analysed by liquid chromatography–mass spectrometry (LC–MS) to compare plasma metabolic changes between the E and IO groups. Multivariate pattern recognition was used to screen the DMs in the plasma of IO cows. Results Compared with normal E cows, there were abnormalities in 20 metabolites in IO cows, including a significantly decreased content (VIP > 1, P < 0.05) of cholic acid, p-chlorophenylalanine, and arachidonic acid, and a significantly increased content (VIP > 1, P < 0.05) of tyramine, betaine, L-phenylalanine, L-glutamate, D-proline, L-alanine, and L-pyrophosphate. Five DMs (cholic acid, D-proline, L-glutamate, L-alanine, and L-pyroglutamic acid) with higher variable importance in projection (VIP) values between groups were validated by ELISA with blind samples of re-selected cows (IO, 50 to 60 d postpartum) and the validated results were consistent with the LC–MS results. Conclusion The 20 DMs in IO cows during the peak of lactation indicated that the pathogenesis of IO was involved in complex metabolic networks and signal transduction pathways. This study provides a basis for further exploration of the pathogenesis and prevention of IO in cows in the future.
Assessing keel bone damage in laying hens by palpation: effects of assessor experience on accuracy, inter-rater agreement and intra-rater consistency

ABSTRACT Accurate assessment is essential when evaluating keel bone damage. Palpation is commonly used to assess keel bone damage in living hens. However, there is little information on the accuracy of assessment of deviations and fractures on different parts of the keel, and on the consistency within, and agreement between, assessors. Crucially, although the importance of experience is commonly emphasized, knowledge on its effect is scarce. Ten assessors with or without prior experience palpated the same 50 75‐wk‐old hens for deviations, medial fractures, and caudal fractures (scored as present/absent). Accuracy, sensitivity, specificity, precision, and negative predictive value were determined by comparing palpation scores to post‐dissection assessment, and then compared between experienced and inexperienced assessors. To determine the effect of the experience gained during the experiment, hens were subsequently re‐assessed. Consistency within, and agreement between, assessors were also determined. Assessors with prior experience were more accurate (proportion of accurately assessed deviations: experienced 0.83 vs. inexperienced 0.79±0.01, P = 0.04; medial fractures: 0.82 vs. 0.68±0.03 in session 1 only, P = 0.04; caudal fractures: 0.41 vs. 0.29±0.03, P = 0.03), and inexperienced assessors classified medial fractures more accurately in session 2 (session 1: 0.68 vs. session 2: 0.77±0.04, P = 0.04). However, effect sizes were small for deviations and even experienced assessors lacked accuracy when assessing caudal fractures. Unexpectedly, deviations tended to be assessed more accurately in session 1 than in session 2, regardless of assessor status (1: 0.83 vs. 2: 0.79±0.01, P = 0.06), suggesting that prolonged assessment contributes to errors. Prior experience decreased specificity and precision of fracture assessment (more unfractured keels were classified as fractured) even though overall accuracy was greater. Intra‐rater consistency was fair to good (0.55 to 0.67) for deviations and medial fractures, but poor to fair (0.36 to 0.44) for caudal fractures, and unaffected by prior experience (P = 0.49 to 0.89). In conclusion, experience improves accuracy to a limited extent but does not guarantee high accuracy for all types of damage. Future research should determine if other training methods (e.g., comparison to post‐dissection scores or to radiographs) improve accuracy.