Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary protein level affects nutrient digestibility and ileal microbiota structure in growing pigs.

This study aimed to determine whether dietary protein content influences pig health as indicated by ileal microbiota structure and coefficients of total tract apparent digestibility (CTTAD) of nutrients. Seventy-two gilts, with an initial body weight of 29.9 ± 1.5 kg, were used in this 42-day feeding study. Pigs were randomly allotted to one of three dietary treatments of corn-soybean meal contained 14, 16 or 18% crude protein (CP). As dietary CP content decreased, the CTTAD of most essential amino acids (AAs), except for arginine and histidine, increased linearly, while those of most nonessential AAs decreased linearly. The concentration of total short-chain fatty acids (SCFA) was higher in pigs fed the diet with 14% CP content than others. Ileal microbiota structure was changed by dietary treatments. In particular, at the phylum level, the relative abundance of Tenericutes in ileal digesta decreased as the dietary protein content reduced, while that of cyanobacteria increased. At the genus level, the relative abundance of Weeksella, Phaseolus acutifolius, Slackia, Sulfurimonas and Aerococcus showed significant differences among the three dietary treatments. In conclusion, ileal microbiota structure was changed by dietary protein content. Moderate reduction of protein intake can benefit gut health by enhancing the gut microbial fermentation and SCFA formation.
Approaches to Encapsulation of Active Food Ingredients in Spray-Drying

Microencapsulation can be used to improve the stability and control the release of dried active food ingredients such as flavors, enzymes, probioticas and oxidation sensitive oils. Spray-drying can be used for encapsulation and powder generation in one step by utilizing different phenomena that occur during drying. Dry emulsion is a classic way to supply encapsulated flavors and protect oxidation sensitive oils. By controlling the formulation and processing, improved flavor stability and releasing profiles can be obtained. A recently developed concept is the application of two-phase aqueous systems for encapsulation of water-soluble materials and probiotic bacteria. During spray-drying, surface-active components interact with the droplet surface, and will coat the powder surface according to their adsorption efficiency. Through understanding of these events, formulation and drying conditions can be designed for optimum coating and encapsulation.
Fault missing rate analysis of the arithmetic residue codes based fault-tolerant FIR filter design

Relative to the Triple Modular Redundancy (TMR) scheme, the arithmetic residue codes based fault-tolerant DSP design consumes much less resources. However, the price for the low resource consumption is the fault missing problem. The basic tradeoff is that, smaller modulus used for the fault checking consumes fewer resources, but the fault missing rate is higher. The relationship between the value of modulus and the fault missing rate is analyzed theoretically in this paper for fault-tolerant FIR filter design, and the results are verified by FPGA implemented fault injections.
Insertion of scFv into the hinge domain of full-length IgG1 monoclonal antibody results in tetravalent bispecific molecule with robust properties

ABSTRACT By simultaneous binding two disease mediators, bispecific antibodies offer the opportunity to broaden the utility of antibody-based therapies. Herein, we describe the design and characterization of Bs4Ab, an innovative and generic bispecific tetravalent antibody platform. The Bs4Ab format comprises a full-length IgG1 monoclonal antibody with a scFv inserted into the hinge domain. The Bs4Ab design demonstrates robust manufacturability as evidenced by MEDI3902, which is currently in clinical development. To further demonstrate the applicability of the Bs4Ab technology, we describe the molecular engineering, biochemical, biophysical, and in vivo characterization of a bispecific tetravalent Bs4Ab that, by simultaneously binding vascular endothelial growth factor and angiopoietin-2, inhibits their function. We also demonstrate that the Bs4Ab platform allows Fc-engineering similar to that achieved with IgG1 antibodies, such as mutations to extend half-life or modulate effector functions.
AntShield: On-Device Detection of Personal Information Exposure

Mobile devices have access to personal, potentially sensitive data, and there is a growing number of applications that transmit this personally identifiable information (PII) over the network. In this paper, we present the AntShield system that performs on-device packet-level monitoring and detects the transmission of such sensitive information accurately and in real-time. A key insight is to distinguish PII that is predefined and is easily available on the device from PII that is unknown a priori but can be automatically detected by classifiers. Our system not only combines, for the first time, the advantages of on-device monitoring with the power of learning unknown PII, but also outperforms either of the two approaches alone. We demonstrate the real-time performance of our prototype as well as the classification performance using a dataset that we collect and analyze from scratch (including new findings in terms of leaks and patterns). AntShield is a first step towards enabling distributed learning of private information exposure.
Optimality-based model of phytoplankton growth and diazotrophy

The notion that excess phosphorus (P) and high irradiance favour pelagic diazotrophy is difficult to reconcile with diazotroph behaviour in laboratory experiments and also with the observed distribution of N2-fixing Trichodesmium, e.g. in the relatively nitrogen (N)-rich North Atlantic Ocean. Nevertheless, this view currently provides the state-of-the-art framework to understand both past dynamics and future evolution of the oceanic fixed N inventory. In an attempt to provide a consistent theoretical underpinning for marine autotrophic N2 fixation we derive controls of diazotrophy from an optimality-based model that accounts for phytoplankton growth and N2 fixation. Our approach differs from existing work in that conditions favourable for diazotrophy are not prescribed but emerge, indirectly, from trade-offs among energy and cellular resource requirements for the acquisition of P, N, and carbon. Our model reproduces laboratory data for a range of ordinary phytoplankton species and Trichodesmium. The model predicts that (1) the optimal strategy for facultative diazotrophy is switching between N2 fixation and using dissolved inorganic nitrogen (DIN) at a threshold DIN concentration; (2) oligotrophy, especially in P and under high light, favours diazotrophy; (3) diazotrophy is compatible with DIN:DIP supply ratios well above Redfield proportions; and (4) communities of diazotrophs competing with ordinary phytoplankton decouple emerging ambient and supply DIN:DIP ratios. Our model predictions appear in line with major observed patterns of diazotrophy in the ocean. The predicted importance of oligotrophy in P extends the present view of N2 fixation beyond a simple control by excess P in the surface ocean.
Pathogen inactivation of Dengue virus in red blood cells using amustaline and glutathione

Dengue virus (DENV) is an arbovirus primarily transmitted through mosquito bite; however, DENV transfusion‐transmitted infections (TTIs) have been reported and asymptomatic DENV RNA–positive blood donors have been identified in endemic countries. DENV is considered a high‐risk pathogen for blood safety. One of the mitigation strategies to prevent arbovirus TTIs is pathogen inactivation. In this study we demonstrate that the amustaline and glutathione (S‐303/GSH) treatment previously found effective against Zika virus in red blood cells (RBCs) is also effective in inactivating DENV.
Prevention of Neurocognitive Impairment in Children Through Newborn Screening for Congenital Hypothyroidism.

Most newborn screening (NBS) programs use serum thyroid-stimulating hormone (TSH) as a primary test, and positive tests are confirmed by serum thyroxine (T4) levels. Infants with confirmed CH are started on treatment with levothyroxine (LT4) to achieve euthyroid state to prevent neurocognitive disabilities. TSH peaks in the first few days after birth and falls rapidly to 4-fold lower levels over the next few days. Mild increases in TSH over the recommended cut-off in NBS protocols for CH are often misclassified as normal. A significant number of these newborns may develop permanent primary hypothyroidism on follow-up. For this reason, many NBS programs order a second specimen in situations where the TSH concentration is mildly elevated between the cut-off and an upper limit of 40 or 50 mU/L [5,6]. A recent study noted that even in USA, many programs do not adjust TSH cut-offs according to the infant’s age, and initial as well as repeat TSH measurements are performed outside the age for which the cut-offs were established [7].
Energy–entropy competition and the effectiveness of stochastic gradient descent in machine learning

ABSTRACT Finding parameters that minimise a loss function is at the core of many machine learning methods. The Stochastic Gradient Descent (SGD) algorithm is widely used and delivers state-of-the-art results for many problems. Nonetheless, SGD typically cannot find the global minimum, thus its empirical effectiveness is hitherto mysterious. We derive a correspondence between parameter inference and free energy minimisation in statistical physics. The degree of undersampling plays the role of temperature. Analogous to the energy–entropy competition in statistical physics, wide but shallow minima can be optimal if the system is undersampled, as is typical in many applications. Moreover, we show that the stochasticity in the algorithm has a non-trivial correlation structure which systematically biases it towards wide minima. We illustrate our argument with two prototypical models: image classification using deep learning and a linear neural network where we can analytically reveal the relationship between entropy and out-of-sample error. GRAPHICAL ABSTRACT
Hierarchical Adversarially Learned Inference

We propose a novel hierarchical generative model with a simple Markovian structure and a corresponding inference model. Both the generative and inference model are trained using the adversarial learning paradigm. We demonstrate that the hierarchical structure supports the learning of progressively more abstract representations as well as providing semantically meaningful reconstructions with different levels of fidelity. Furthermore, we show that minimizing the Jensen-Shanon divergence between the generative and inference network is enough to minimize the reconstruction error. The resulting semantically meaningful hierarchical latent structure discovery is exemplified on the CelebA dataset. There, we show that the features learned by our model in an unsupervised way outperform the best handcrafted features. Furthermore, the extracted features remain competitive when compared to several recent deep supervised approaches on an attribute prediction task on CelebA. Finally, we leverage the model's inference network to achieve state-of-the-art performance on a semi-supervised variant of the MNIST digit classification task.
Magnetic Resonance Imaging Plaque Hemorrhage for Risk Stratification in Carotid Artery Disease With Moderate Risk Under Current Medical Therapy

Background and Purpose— Magnetic resonance imaging (MRI)–defined carotid plaque hemorrhage (MRIPH) can predict recurrent cerebrovascular ischemic events in severe symptomatic carotid stenosis. It is less clear whether MRIPH can improve risk stratification despite optimized medical secondary prevention in those with moderate risk. Methods— One-hundred fifty-one symptomatic patients with 30% to 99% carotid artery stenosis (median age: 77, 60.5% men) clinically deemed to not benefit from endarterectomy were prospectively recruited to undergo MRI and clinical follow-up (mean, 22 months). The clinical carotid artery risk score could be evaluated in 88 patients. MRIPH+ve was defined as plaque intensity >150% that of adjacent muscle. Survival analyses were performed with recurrent infarction (stroke or diffusion-positive cerebral ischemia) as the main end point. Results— Fifty-five participants showed MRIPH+ve; 47 had low, 36 intermediate, and 5 high carotid artery risk scores. Cox regression showed MRIPH as a strong predictor of future infarction (hazard ratio, 5.2; 95% confidence interval, 1.64–16.34; P=0.005, corrected for degree of stenosis), also in the subgroup with 50% to 69% stenosis (hazard ratio, 4.1; 95% confidence interval, 1–16.8; P=0.049). The absolute risk of future infarction was 31.7% at 3 years in MRIPH+ve versus 1.8% in patients without (P<0.002). MRIPH increased cumulative risk difference of future infarction by 47.1% at 3 years in those with intermediate carotid artery risk score (P=0.004). Conclusions— The study confirms MRIPH to be a powerful risk marker in symptomatic carotid stenosis with added value over current risk scores. For patients undergoing current secondary prevention medication with clinically uncertain benefit from recanalization, that is, those with moderate degree stenosis and intermediate carotid artery risk scores, MRIPH offers additional risk stratification.
Challenging the Time Complexity of Exact Subgraph Isomorphism for Huge and Dense Graphs with VF3

Graph matching is essential in several fields that use structured information, such as biology, chemistry, social networks, knowledge management, document analysis and others. Except for special classes of graphs, graph matching has in the worst-case an exponential complexity; however, there are algorithms that show an acceptable execution time, as long as the graphs are not too large and not too dense. In this paper we introduce a novel subgraph isomorphism algorithm, VF3, particularly efficient in the challenging case of graphs with thousands of nodes and a high edge density. Its performance, both in terms of time and memory, has been assessed on a large dataset of 12,700 random graphs with a size up to 10,000 nodes, made publicly available. VF3 has been compared with four other state-of-the-art algorithms, and the huge experimentation required more than two years of processing time. The results confirm that VF3 definitely outperforms the other algorithms when the graphs become huge and dense, but also has a very good performance on smaller or sparser graphs.
The effect of dialysis type on left atrial functions in patients with end‐stage renal failure: A propensity score‐matched analysis

Despite the widespread use of both hemodialysis (HD) and peritoneal dialysis (PD), there is no study comparing the effects of these dialysis methods on the left atrial (LA) volume and functions. In this study, we investigated the impact of different dialysis methods on the LA volume and function in the patients exposed to chronic pressure overload and volume overload.
INTEGRATED MANAGEMENT OF CROP RESIDUE AND N FERTILIZER FOR WHEAT PRODUCTION

A field experiment was conducted at Agricultural Research Farm, KPK Agricultural University, Peshawar, Pakistan during winter 2005-2006. The treatments consisted of crop residue (stover & legume residue), two type of fertilizer-N (NH4N & NO3-N) and their application time i.e. at sowing and 2 nd node appearance stage. Higher spikes m -2 and grain yield were recorded for nitrate-N application in split at the rate of 100 kg ha -1 in combination with legume residue. Likewise, the highest grains spike -1 was recorded for legume and cereal residue application along with nitrate and ammonium N application at the rate of 100 kg ha -1 , respectively. However, 1000 grain weight was higher for legume residue along with split application of ammonium-N at the rate of 100 kg ha -1 . Planned mean comparisons showed that control plots produced significantly less spikes m -2 , grains spike -1 , 1000 grain weight and grain yield as compared to mean of the rest of the treatments. Likewise, legume alone enhanced spikes production as compared to cereal in combination with N. Similarly, legume alone also performed better than cereal alone for improving grain weight. In the same manner, residue plus nitrate-N produced higher grain yield as compared to residue plus ammonium-N.
Distributions of particulate Heme b in the Atlantic and Southern Oceans—Implications for electron transport in phytoplankton

Concentrations of heme b, the iron‐containing component of b‐type hemoproteins, ranged from < 0.4 to 5.3 pM with an average of 1.18 ± 0.8 pM (± 1σ; n = 86) in the Iceland Basin (IB), from < 0.4 to 19.1 pM with an average of 2.24 ± 1.67 pM (n = 269) in the tropical northeast Atlantic (TNA) and from 0.6 to 21 pM with an average of 5.1 ± 4.8 pM (n = 34) in the Scotia Sea (SS). Heme b concentrations were enhanced in the photic zone and decreased with depth. Heme b concentrations correlated positively with chlorophyll a (chl a) in the TNA (r = 0.41, p < 0.01, n = 269). Heme b did not correlate with chl a in the IB or SS. In the IB and SS, stations with high‐chlorophyll and low‐nutrient (Fe and/or Si) concentrations exhibited low heme b concentrations relative to particulate organic carbon (< 0.1 μmol mol−1), and high chl a:heme b ratios (> 500). High chl a:heme b ratios resulted from relative decreases in heme b, suggesting proteins such as cytochrome b6f, the core complex of photosystem II, and eukaryotic nitrate reductase were depleted relative to proteins containing chlorophyll such as the eukaryotic light‐harvesting antenna. Relative variations in heme b, particulate organic carbon, and chl a can thus be indicative of a physiological response of the phytoplankton community to the prevailing growth conditions, within the context of large‐scale changes in phytoplankton community composition.
Telemedicine Can Replace the Neurologist on a Mobile Stroke Unit

Background and Purpose— The BEST-MSU study (Benefits of Stroke Treatment Delivered Using a Mobile Stroke Unit) is a comparative effectiveness trial in patients randomized to mobile stroke unit or standard management. A substudy tested interrater agreement for tissue-type plasminogen activator eligibility between a telemedicine vascular neurologist and onboard vascular neurologist. Methods— On scene, both the telemedicine vascular neurologist and onboard vascular neurologist independently evaluated the patient, documenting their tissue-type plasminogen activator treatment decision, National Institutes of Health Stroke Scale score, and computed tomographic interpretation. Agreement was determined using Cohen &kgr; statistic. Telemedicine-related technical failures that impeded remote assessment were recorded. Results— Simultaneous and independent telemedicine vascular neurologist and onboard vascular neurologist assessment was attempted in 174 patients. In 4 patients (2%), the telemedicine vascular neurologist could not make a decision because of technical problems. The telemedicine vascular neurologist agreed with the onboard vascular neurologist on 88% of evaluations (&kgr;=0.73). Conclusions— Remote telemedicine vascular neurologist assessment is reliable and accurate, supporting either telemedicine vascular neurologist or onboard vascular neurologist assessment on our mobile stroke unit. Clinical Trial Registration— URL: http://www.clinicaltrials. gov. Unique identifier: NCT02190500.
Evaluation of the Commercial Kit SIRE Nitratase for detecting resistant Mycobacterium tuberculosis in Brazil.

INTRODUCTION: This study aimed to evaluate a new commercial kit, Kit SIRE Nitratase-PlastLabor, for testing the drug susceptibility of clinical Mycobacterium tuberculosis isolates. METHODS: The accuracy of the Kit SIRE Nitratase was evaluated by examining the susceptibility (streptomycin, isoniazid, rifampicin, and ethambutol) of 40 M. tuberculosis isolates, using the proportion method with Lowenstein-Jensen medium or the BACTEC MGIT 960 system. RESULTS: The detection accuracy for streptomycin, isoniazid, rifampicin, and ethambutol was 95%, 97.5%, 100%, and 80%, respectively. CONCLUSIONS: The exceptional accuracy demonstrated by Kit SIRE Nitratase for isoniazid and rifampicin makes the kit an attractive option for screening M. tuberculosis strain resistance.
Household-level factors associated with relapse following discharge from treatment for moderate acute malnutrition

Abstract Factors associated with relapse among children who are discharged after reaching a threshold denoted ‘recovered’ from moderate acute malnutrition (MAM) are not well understood. The aim of this study was to identify factors associated with sustained recovery, defined as maintaining a mid-upper-arm circumference≥12·5 cm for 1 year after release from treatment. On the basis of an observational study design, we analysed data from an in-depth household (HH) survey on a sub-sample of participants within a larger cluster randomised controlled trial (cRCT) that followed up children for 1 year after recovery from MAM. Out of 1497 children participating in the cRCT, a subset of 315 children participated in this sub-study. Accounting for other factors, HH with fitted lids on water storage containers (P=0·004) was a significant predictor of sustained recovery. In addition, sustained recovery was better among children whose caregivers were observed to have clean hands (P=0·053) and in HH using an improved sanitation facility (P=0·083). By contrast, socio-economic status and infant and young child feeding practices at the time of discharge and HH food security throughout the follow-up period were not significant. Given these results, we hypothesise that improved water, sanitation and hygiene conditions in tandem with management of MAM through supplemental feeding programmes have the possibility to decrease relapse following recovery from MAM. Furthermore, the absence of associations between relapse and nearly all HH-level factors indicates that the causal factors of relapse may be related mostly to the child’s individual, underlying health and nutrition status.
Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria

Gene control systems sometimes interpret multiple signals to set the expression levels of the genes they regulate. In rare instances, ligand-binding riboswitch aptamers form tandem arrangements to approximate the function of specific two-input Boolean logic gates. Here, we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria. The existence of sophisticated all-RNA regulatory systems that sense two ancient ribonucleotide derivatives to control synthesis of RNA molecules supports the hypothesis that RNA World organisms could have managed a complex metabolic state without the assistance of protein regulatory factors.