Miracle-dz/UniFAR-FTUs huggingface dataset:
Superficial and deep changes of histology, texture and particle size distribution in broiler wooden breast muscle during refrigerated storage

ABSTRACT Recently the poultry industry faced an emerging muscle abnormality termed wooden breast (WB), the prevalence of which has dramatically increased in the past few years. Considering the incomplete knowledge concerning this condition and the lack of information on possible variations due to the intra‐fillet sampling locations (superficial vs. deep position) and aging of the samples, this study aimed at investigating the effect of 7‐d storage of broiler breast muscles on histology, texture, and particle size distribution, evaluating whether the sampling position exerts a relevant role in determining the main features of WB. With regard to the histological observations, severe myodegeneration accompanied by accumulation of connective tissue was observed within the WB cases, irrespective of the intra‐fillet sampling position. No changes in the histological traits took place during the aging in either the normal or the WB samples. As to textural traits, although a progressive tenderization process took place during storage (P ≤ 0.001), the differences among the groups were mainly detected when raw meat rather than cooked was analyzed, with the WB samples exhibiting the highest (P ≤ 0.001) 80% compression values. In spite of the increased amount of connective tissue components in the WB cases, their thermally labile cross‐links will account for the similar compression and shear‐force values as normal breast cases when measured on cooked samples. Similarly, the enlargement of extracellular matrix and fibrosis might contribute in explaining the different fragmentation patterns observed between the superficial and the deep layer in the WB samples, with the superficial part exhibiting a higher amount of larger particles and an increase in particles with larger size during storage, compared to normal breasts.
Black Pepper and Health Claims: A Comprehensive Treatise

For millennia, spices have been an integral part of human diets and commerce. Recently, the widespread recognition of diet-health linkages bolsters their dietary importance. The bioactive components present in them are of considerable significance owing to their therapeutic potential against various ailments. They provide physiological benefits or prevent chronic ailment in addition to the fundamental nutrition and often included in the category of functional foods. Black pepper (Piper Nigrum L.) is an important healthy food owing to its antioxidant, antimicrobial potential and gastro-protective modules. Black pepper, with piperine as an active ingredient, holds rich phytochemistry that also includes volatile oil, oleoresins, and alkaloids. More recently, cell-culture studies and animal modeling predicted the role of black pepper against number of maladies. The free-radical scavenging activity of black pepper and its active ingredients might be helpful in chemoprevention and controlling progression of tumor growth. Additionally, the key alkaloid components of Piper Nigrum, that is, piperine assist in cognitive brain functioning, boost nutrient's absorption and improve gastrointestinal functionality. In this comprehensive treatise, efforts are made to elucidate the antioxidant, antimicrobial, anti-inflammatory, gastro-protective, and antidepressant activities of black pepper. Moreover, the synergistic interaction of black pepper with different drugs and nutrients is the limelight of the manuscript. However, the aforementioned health-promoting benefits associated with black pepper are proven in animal modeling. Thus, there is a need to conduct controlled randomized trials in human subjects, cohort studies, and meta-analyses. Such future studies would be helpful in recommending its application in diet-based regimens to prevent various ailments.
Biotechnological potential of insect fatty acid-modifying enzymes

Abstract There are more than one million described insect species. This species richness is reflected in the diversity of insect metabolic processes. In particular, biosynthesis of secondary metabolites, such as defensive compounds and chemical signals, encompasses an extraordinarily wide range of chemicals that are generally unparalleled among natural products from other organisms. Insect genomes, transcriptomes and proteomes thus offer a valuable resource for discovery of novel enzymes with potential for biotechnological applications. Here, we focus on fatty acid (FA) metabolism-related enzymes, notably the fatty acyl desaturases and fatty acyl reductases involved in the biosynthesis of FA-derived pheromones. Research on insect pheromone-biosynthetic enzymes, which exhibit diverse enzymatic properties, has the potential to broaden the understanding of enzyme specificity determinants and contribute to engineering of enzymes with desired properties for biotechnological production of FA derivatives. Additionally, the application of such pheromone-biosynthetic enzymes represents an environmentally friendly and economic alternative to the chemical synthesis of pheromones that are used in insect pest management strategies.
The effects of human keratinocyte coculture on human adipose‐derived stem cells

The potential for adipose‐derived stem cells to differentiate into keratinocyte‐like cells has recently been receiving attention, stemming from the hypothesis that a bioengineered skin may be manufactured from these readily available mesenchymal stem cells. This study was conducted to evaluate the influence of human keratinocyte non‐contact coculture on hADSCs. Human epidermal keratinocytes and hADSCs obtained by lipoaspiration were cultured in keratinogenic growth media, which were divided into the following groups: human adipose‐derived stem cell (hADSC) monoculture, non‐contact coculture of hADSCs and human keratinocytes and keratinocyte monoculture. Cell proliferation was assessed, and keratogenicity was analysed through immunocytochemistry and polymerase chain reaction of early, intermediate and late keratogenic markers. hADSCs cocultured with keratinocytes displayed enhanced proliferation compared with the monoculture group. After a 7‐day coculture period, immunohistochemistry and polymerase chain reaction findings revealed the presence of specific keratinocyte markers in the coculture group. This study demonstrates that hADSCs cocultured with keratinocytes have the capacity to transdifferentiate into keratinocyte lineage cells, and suggests that adipose tissue may be a source of keratinocytes that may further be used in structuring the bioengineered skin.
Quantification of circulating Mycobacterium tuberculosis antigen peptides allows rapid diagnosis of active disease and treatment monitoring

Significance Active Mycobacterium tuberculosis (Mtb) infections represent a significant global health threat, but can be difficult to diagnose and manage owing to the nonquantitative nature and relatively poor performance of current frontline sputum-based diagnostic assays, which can be further degraded by certain Mtb manifestations. This study describes the development of a rapid and quantitative blood-based assay with high sensitivity and specificity for active Mtb infections that can be used to monitor responses to antimycobacterial therapy. Our method combines antibody-labeled, energy-focusing nanodisks with high-throughput mass spectrometry to enhance the detection of Mtb-specific peptides in digested serum samples, and should allow rapid clinical translation. This approach also should be applicable to other infectious diseases, particularly those for which conventional immunoassays exhibit suboptimal performance. Tuberculosis (TB) is a major global health threat, resulting in an urgent unmet need for a rapid, non–sputum-based quantitative test to detect active Mycobacterium tuberculosis (Mtb) infections in clinically diverse populations and quickly assess Mtb treatment responses for emerging drug-resistant strains. We have identified Mtb-specific peptide fragments and developed a method to rapidly quantify their serum concentrations, using antibody-labeled and energy-focusing porous discoidal silicon nanoparticles (nanodisks) and high-throughput mass spectrometry (MS) to enhance sensitivity and specificity. NanoDisk-MS diagnosed active Mtb cases with high sensitivity and specificity in a case-control study with cohorts reflecting the complexity of clinical practice. Similar robust sensitivities were obtained for cases of culture-positive pulmonary TB (PTB; 91.3%) and extrapulmonary TB (EPTB; 92.3%), and the sensitivities obtained for culture-negative PTB (82.4%) and EPTB (75.0%) in HIV-positive patients significantly outperformed those reported for other available assays. NanoDisk-MS also exhibited high specificity (87.1–100%) in both healthy and high-risk groups. Absolute quantification of serum Mtb antigen concentration was informative in assessing responses to antimycobacterial treatment. Thus, a NanoDisk-MS assay approach could significantly improve the diagnosis and management of active TB cases, and perhaps other infectious diseases as well.
Coronary evaginations and peri-scaffold aneurysms following implantation of bioresorbable scaffolds: incidence, outcome, and optical coherence tomography analysis of possible mechanisms.

BACKGROUND Peri-stent coronary evaginations may disturb flow and have been proposed as possible risk factor for late stent thrombosis. We describe incidence, predictors, and possible mechanisms of coronary evaginations 12 months after implantation of bioresorbable vascular scaffolds (BVS). METHODS AND RESULTS One hundred and two BVS implanted in 90 patients (age 63 ± 13 years, 71 males, 14 diabetics) were analysed with angiography and optical coherence tomography (OCT) 12 months after implantation. Evaginations were identified as any hollow in the luminal vessel contour between well-apposed struts and were classified as major when extending ≥3 mm with a depth ≥10% of the BVS diameter. Fifty-five (54%) of the BVS (50(56%) of the patients) had at least one evagination (6.1 ± 6.2 evaginations per BVS), with a mean volume of 1.9 ± 1.9 mm(3). Major evaginations were only found in one patient, and in-BVS aneurysms in three patients (4BVS). The presence of evaginations was strongly associated with that of malapposition (P = 0.003) and strut fractures (P = 0.01). No association could be shown between the presence and volume of the evaginations and any clinical variable or the presence of uncovered struts (P > 0.5). Peri-strut low-intensity areas (PSLIA) were present in 29 (53%) of the BVS with evaginations and 12 (26%) of those without (P = 0.0049); their presence was independently associated with the presence, the number (P < 0.003) and volume of the evaginations (P = 0.004) and with that of strut fracture. CONCLUSIONS Optical coherence tomography-detected evaginations are relatively common after BVS implantation, but, as for modern drug-eluting metallic stents, major evaginations are very rare. Optical coherence tomography evidence of immature neointima and strut fractures were associated with more severe development of evaginations.
Stochastic Ratcheting on a Funneled Energy Landscape is Necessary for Highly Efficient Contractility of Actomyosin Force Dipoles

Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the free energy gain following passive cross-linker binding, which, even in the absence of active fluctuations, provides a thermodynamic drive towards highly overlapping filamentous states. In this work, we shed light on this phenomenon, showing that passive cross-linkers, when considered in the context of two anti-parallel filaments, generate noticeable contractile forces. However, as binding free energy of cross-linkers is increased, a sharp onset of kinetic arrest follows, greatly diminishing effectiveness of this contractility mechanism, allowing the network to contract only with weakly resisting tensions at its boundary. We have carried out stochastic simulations elucidating this mechanism, followed by a mean-field treatment that predicts how contractile forces asymptotically scale at small and large binding energies, respectively. Furthermore, when considering an active contractile filament pair, based on non-muscle myosin II, we found that the non-processive nature of these motors leads to highly inefficient force generation, due to recoil slippage of the overlap during periods when the motor is dissociated. However, we discovered that passive cross-linkers can serve as a structural ratchet during these unbound motor time spans, resulting in vast force amplification. Our results shed light on the non-equilibrium effects of transiently binding proteins in biological active matter, as observed in the non-muscle actin cytoskeleton, showing that highly efficient contractile force dipoles result from synergy of passive cross-linker and active motor dynamics, via a ratcheting mechanism on a funneled energy landscape.
JeCache: Just-Enough Data Caching with Just-in-Time Prefetching for Big Data Applications

Big data clusters introduce an intermediate cache layer between the computing frameworks and the underlying distributed file systems, to enable upper-level applications or end users to efficiently access big datasets in cache and effectively share them among different computing frameworks. As caches are shared by multiple applications or end users, directly applying existing on-demand caching strategies will result in intense conflicts, when big datasets are cached as a whole. Meanwhile, big data applications usually involve massive numbers of file scans, cached-in data blocks may have little chance of being accessed before they are cached out to make way for other on-demand data blocks. Thus, it is unwise to cache data blocks long before they are actually accessed. In this paper, we propose a novel just-enough big data caching scheme for just-in-time block prefetching to improve the cache effectiveness of big data clusters. With just-in-time block prefetching, a block is cached in just before the task begins to process the block, rather than being cached in along with other blocks of the same dataset being processed. We monitor block accesses to measure the average processing time of data blocks, and then estimate the minimal number of blocks that should be kept in cache for a big dataset, so that the speed of data processing matches with that of data prefetching, and each upper-level task can obtain its input blocks from cache just in time. Our experimental results show that the proposed cache method can restrain over-requirement of cache resources in big data applications, and provides the same performance improvement as when all data blocks are cached.
The Clinical Inadequacy of the Placebo Model and the Development of an Alternative Conceptual Framework

Placebo effects are often attributed to clinical interactions and contextual factors that affect expectations of the patient about the treatment and result in symptom changes. The prevailing conceptualization consists of an undifferentiated placebo response that needs to be minimized in controlled investigations and maximized in clinical practice. However, treatment outcome is the cumulative result of the interaction of several classes of variables with a selected treatment: living conditions (housing, nutrition, work environment, social support), patient characteristics (age, sex, genetics, general health conditions, personality, well-being), illness features and previous therapeutic experience, self-management, and treatment setting (physician's attitude and attention, illness behavior). Such variables may be therapeutic or countertherapeutic, and are unlikely to be simply additive. In certain patients their interactive combination may lead to clinical improvement, whereas in other cases it may produce no effect, and, in a third group, it may lead to worsening of the condition. Maximizing patients' expectations does not necessarily result in sustained effects and, in due course, may actually lead to worsening of the condition (violation of expectations). In this paper, we outline a multifactorial conceptual model that may have implications for the design of clinical trials as well as for clinical practice, with special reference to psychopharmacology and psychotherapy. The effects of drug treatment may be potentiated by specific nonpharmacological treatment strategies, and this synergism may disclose significant differences against placebo. Medical outcomes may be unsatisfactory not because technical interventions are missing, but because our conceptual models and thinking are inadequate.
Local Binary Patterns for Document Forgery Detection

Document forgery is an increasing problem for both the public administration and private companies. It represents substantial losses in time and economical resources. Classical solutions to this problem such as watermarks or other integrated security patterns can not be applied in general for any unknown incoming document due to the large variability on types of documents. In that scenario it is important to resort to forensic techniques to seek and analyze inconsistencies on the intrinsic features of the document image. In this paper we present a classification-based approach for forgery detection. We use uniform Local Binary Patterns (LBP) to capture discriminant texture features that are common on forged regions. Besides, we combine multiple descriptors from neighboring regions to model contextual information. Results using Support Vector Machines (SVM) for patch classification show that we are able to detect several types of forgeries in a wide range of types of documents.
Gated Convolutional Recurrent Neural Networks for Multilingual Handwriting Recognition

In this paper, we propose a new neural network architecture for state-of-the-art handwriting recognition, alternative to multi-dimensional long short-term memory (MD-LSTM) recurrent neural networks. The model is based on a convolutional encoder of the input images, and a bidirectional LSTM decoder predicting character sequences. In this paradigm, we aim at producing generic, multilingual and reusable features with the convolutional encoder, leveraging more data for transfer learning. The architecture is also motivated by the need for a fast training on GPUs, and the requirement of a fast decoding on CPUs. The main contribution of this paper lies in the convolutional gates in the encoder, enabling hierarchical context-sensitive feature extraction. The experiments on a large benchmark including seven languages show a consistent and significant improvement of the proposed approach over our previous production systems. We also report state-of-the-art results on line and paragraph level recognition on the IAM and Rimes databases.
Supplement to : Optimally controlling the human connectome : the role of network topology

connectome: the role of network topology Richard F. Betzel, Shi Gu, John D. Medaglia, Fabio Pasqualetti, and Danielle S. Bassett∗1,4 1 Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104 2 Department of Psychology, University of Pennsylvania, Philadelphia, PA, 19104 3 Department of Mechanical Engineering, University of California, Riverside, Riverside, CA, 92521 4 Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA, 19104
An Effective Power Grid Optimization Approach for the Electromigration Reliability

An effective optimization approach for the electromigration (EM) reliability in power grid (PG) has been presented in this paper. With core technology development and the key feature size of integrated circuits decreasing, it is more serious for the EM-induced failure occurrence in the entire PG. However, previous PG studies focus on supply noise optimization and neglect the EM influence in lines, especially transient effects of EM phenomenon, and researches in EM reliability are purely confined to local branches or segments now. In the paper, we propose an optimization approach to dealing with EM failure problem in the entire PG, which could effectively lengthen lifetime of the entire circuit in the case that supply noise can be guaranteed. In addition, a composite method flow has been proposed to illustrate the connection between the two optimizations. Experimental results show that our proposed method achieves the goal of transient EM analysis and optimization with supply noise constraints guaranteed. Meanwhile, COMSOL simulation results also confirm effectiveness of the PG optimization approach. For several different scale PG benchmarks, our method can lengthen lifetime of the entire circuit approximately by 10% with the area overhead increased only by 1% within reasonable runtime.
Schizotypal Traits in Healthy Women Predict Prefrontal Activation Patterns during a Verbal Fluency Task: A Near-Infrared Spectroscopy Study

Background/Aims: Previous functional neuroimaging studies have reported that patients with schizophrenia show reduced prefrontal activation during cognitive tasks whereas patients with schizotypal personality disorder (SPD) show preserved or even increased right prefrontal activation, compared to healthy controls; on the other hand, reduced hemispheric laterality is considered to be common to these two disorders. The aim of this study was to examine the possible association between schizotypal traits at a nonclinical level and prefrontal activation patterns during a letter version of the verbal fluency task (VFT). Methods: We examined the relationships of schizotypal traits as measured by the Schizotypal Personality Questionnaire (SPQ) in a nonclinical female population with prefrontal activation patterns during the VFT, using near-infrared spectroscopy. Twenty-seven healthy participants were divided into high (n = 14) and low (n = 13) SPQ groups by the median split of the total SPQ score. Results: Compared to the low SPQ group, the high SPQ group showed significantly larger right prefrontal activation during the performance of the VFT, leading to more bilateral activation. Conclusion: Our results suggest that schizotypal traits at a nonclinical level may be related to relative right prefrontal laterality with overall prefrontal activation being preserved, consistent with previous findings obtained by studies of patients with SPD.
Ultrastructural Characterization of Membrane Rearrangements Induced by Porcine Epidemic Diarrhea Virus Infection

The porcine epidemic diarrhea virus (PEDV) is a coronavirus (CoV) belonging to the α-CoV genus and it causes high mortality in infected sucking piglets, resulting in substantial losses in the farming industry. CoV trigger a drastic reorganization of host cell membranes to promote their replication and egression, but a detailed description of the intracellular remodeling induced by PEDV is still missing. In this study, we examined qualitatively and quantitatively, using electron microscopy, the intracellular membrane reorganization induced by PEDV over the course of an infection. With our ultrastructural approach, we reveal that, as most of CoV, PEDV initially forms double-membrane vesicles (DMVs) and convoluted membranes (CMs), which probably serve as replication/transcription platforms. Interestingly, we also found that viral particles start to form almost simultaneously in both the endoplasmic reticulum and the large virion-containing vacuoles (LVCVs), which are compartments originating from the Golgi, confirming that α-CoV assemble indistinguishably in two different organelles of the secretory pathway. Moreover, PEDV virons appear to have an immature and a mature form, similar to another α-CoV the transmissible gastroenteritis coronavirus (TGEV). Altogether, our study underlies the similarities and differences between the lifecycle of α-CoV and that of viruses belonging to other CoV subfamilies.