Miracle-dz/UniFAR-FTUs huggingface dataset:
Exceptionally Long CDR3H Are Not Isotype Restricted in Bovine Immunoglobulins

Exceptionally long third complementarity determining regions of the heavy chain (CDR3H) were previously described as a specificity of bovine IgG and IgM immunoglobulins. In addition, the genomic organization of the immunoglobulin heavy chain locus remains to be elucidated with a special focus on the number of variable segments (IGHV). By analyzing the variable regions according to the isotype-specific PCR using cDNA-PCR, we were able to prove the existence of exceptional long CDR3H in all bovine isotypes. The corresponding sequences of three distinct amplicons were grouped according to the length of the CDR3H. Sequences of CDR3H possessed 5 to 10, 12 to 31 or at least 48 amino acid residues. Long and mid-length CDR3H were composed of mainly hydrophilic amino acid residues, while short CDR3H also contained hydrophobic amino acid residues. All sequences with long CDR3H were related to the germline variable segment 10. Using the current genome assembly, Bos taurus NCBI build 6.1, the genomic organization of the bovine immunoglobulin heavy-chain locus was analyzed. A main locus was investigated on BTA21. Exons coding for variable, diversity, and joining segments, as well as for the constant regions of different isotypes, were also localized on BTA7, BTA8, and BTA20. Together with the information from unplaced contigs, 36 IGHV were detected of which 13 are putatively functional. Phylogenetic analysis revealed two bovine IGHV families (boVH1, boVH2). Thus, the existence of the two bovine families suggested was demonstrated, where boVH1 comprises all functional segments. This study substantially improves the understanding of the generation of immunoglobulin diversity in cattle.
Automated flow for compressing convolution neural networks for efficient edge-computation with FPGA

Deep convolutional neural networks (CNN) based solutions are the current state- of-the-art for computer vision tasks. Due to the large size of these models, they are typically run on clusters of CPUs or GPUs. However, power requirements and cost budgets can be a major hindrance in adoption of CNN for IoT applications. Recent research highlights that CNN contain significant redundancy in their structure and can be quantized to lower bit-width parameters and activations, while maintaining acceptable accuracy. Low bit-width and especially single bit-width (binary) CNN are particularly suitable for mobile applications based on FPGA implementation, due to the bitwise logic operations involved in binarized CNN. Moreover, the transition to lower bit-widths opens new avenues for performance optimizations and model improvement. In this paper, we present an automatic flow from trained TensorFlow models to FPGA system on chip implementation of binarized CNN. This flow involves quantization of model parameters and activations, generation of network and model in embedded-C, followed by automatic generation of the FPGA accelerator for binary convolutions. The automated flow is demonstrated through implementation of binarized "YOLOV2" on the low cost, low power Cyclone- V FPGA device. Experiments on object detection using binarized YOLOV2 demonstrate significant performance benefit in terms of model size and inference speed on FPGA as compared to CPU and mobile CPU platforms. Furthermore, the entire automated flow from trained models to FPGA synthesis can be completed within one hour.
SIFT: Design and analysis of a fault-tolerant computer for aircraft control

SIFT (Software Implemented Fault Tolerance) is an ultrareliable computer for critical aircraft control applications that achieves fault tolerance by the replication of tasks among processing units. The main processing units are off-the-shelf minicomputers, with standard microcomputers serving as the interface to the I/O system. Fault isolation is achieved by using a specially designed redundant bus system to interconnect the proeessing units. Error detection and analysis and system reconfiguration are performed by software. Iterative tasks are redundantly executed, and the results of each iteration are voted upon before being used. Thus, any single failure in a processing unit or bus can be tolerated with triplication of tasks, and subsequent failures can be tolerated after reconfiguration. Independent execution by separate processors means that the processors need only be loosely synchronized, and a novel fault-tolerant synchronization method is described. The SIFT software is highly structured and is formally specified using the SRI-developed SPECIAL language. The correctness of SIFT is to be proved using a hierarchy of formal models. A Markov model is used both to analyze the reliability of the system and to serve as the formal requirement for the SIFT design. Axioms are given to characterize the high-level behavior of the system, from which a correctness statement has been proved. An engineering test version of SIFT is currently being built.
Antiaging Effect of Metformin on Brain in Naturally Aged and Accelerated Senescence Model of Rat.

Metformin, a biguanide, is a widely used antidiabetic drug, which inhibits gluconeogenesis and is used to treat hyperglycemia in type 2 diabetes. Through activation of AMPK (AMP-activated protein kinase) pathway, metformin also mimics caloric restriction health benefits. Aging causes substantial molecular to morphological changes in brain, the brain cells being more susceptible toward oxidative stress mediated damages due to the presence of high lipid content and higher oxygen consumption. Wistar rats (naturally aged and d-galactose induced rat model) were supplemented with metformin (300 mg/kg b.w. orally) for 6 weeks. The biomarkers of oxidative stress such as antioxidant capacity (ferric reducing antioxidant potential [FRAP]), malondialdehyde (MDA), reduced glutathione (GSH), protein carbonyl (PCO), reactive oxygen species (ROS), acetylcholinesterase (AChE) activity, and nitric oxide (NO) were measured in brain tissues of control and experimental groups. The results indicate that metformin treatment augmented the levels of FRAP and GSH in naturally aged, and d-gal induced aging model groups compared to the respective controls. In contrast, metformin treated groups exhibited significant reduction in MDA, PCO, ROS, and NO levels and a significant increase in AChE activity in induced aging rats. The administration of d-galactose upregulated the expression of sirtuin-2, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) and downregulated the expression of Beclin-1. Metformin supplementation downregulated the d-galactose induced expressions of sirtuin-2, IL-6, and TNF-α expression, whereas upregulated the Beclin-1 expression. Our data confirm that metformin restores the antioxidant status and improves healthy brain aging through the activation of autophagy and reduction in inflammation.
Prospective Clinical Trial Assessing Species-Specific Efficacy of Artemether-Lumefantrine for the Treatment of Plasmodium malariae, Plasmodium ovale, and Mixed Plasmodium Malaria in Gabon

ABSTRACT Treatment recommendations for Plasmodium malariae and Plasmodium ovale malaria are largely based on anecdotal evidence. The aim of this prospective study, conducted in Gabon, was to systematically assess the efficacy and safety of artemether-lumefantrine for the treatment of patients with uncomplicated P. malariae or P. ovale species monoinfections or mixed Plasmodium infections. Patients with microscopically confirmed P. malariae, P. ovale, or mixed-species malaria with at least one of these two Plasmodium species were treated with an oral, fixed-dose combination of artemether-lumefantrine for 3 consecutive days. The primary endpoints were per-protocol PCR-corrected adequate clinical and parasitological response (ACPR) on days 28 and 42. Tolerability and safety were recorded throughout the follow-up period. Seventy-two participants (42 male and 30 female) were enrolled; 62.5% of them had PCR-corrected mixed Plasmodium infections. Per protocol, PCR-corrected ACPR rates were 96.6% (95% confidence interval [CI], 91.9 to 100) on day 28 and 94.2% (95% CI, 87.7 to 100) on day 42. Considering Plasmodium species independently from their coinfecting species, day 42 ACPR rates were 95.5% (95% CI, 89.0 to 100) for P. falciparum, 100% (exact CI, 84.6 to 100) for P. malariae, 100% (exact CI, 76.8 to 100) for P. ovale curtisi, and 90.9% (95% CI, 70.7 to 100) for P. ovale wallikeri. Study drug-related adverse events were generally mild or moderate. In conclusion, this clinical trial demonstrated satisfying antimalarial activity of artemether-lumefantrine against P. ovale wallikeri, P. ovale curtisi, P. malariae, and mixed Plasmodium infections, with per-protocol efficacies of 90% to 100% and without evident tolerability or safety concerns. (This trial was registered in the clinical study database ClinicalTrials.gov under the identifier NCT02528279.)
Population Differentiation and Species Formation in the Deep Sea: The Potential Role of Environmental Gradients and Depth

Ecological speciation probably plays a more prominent role in diversification than previously thought, particularly in marine ecosystems where dispersal potential is great and where few obvious barriers to gene flow exist. This may be especially true in the deep sea where allopatric speciation seems insufficient to account for the rich and largely endemic fauna. Ecologically driven population differentiation and speciation are likely to be most prevalent along environmental gradients, such as those attending changes in depth. We quantified patterns of genetic variation along a depth gradient (1600-3800m) in the western North Atlantic for a protobranch bivalve ( Nuculaatacellana ) to test for population divergence. Multilocus analyses indicated a sharp discontinuity across a narrow depth range, with extremely low gene flow inferred between shallow and deep populations for thousands of generations. Phylogeographical discordance occurred between nuclear and mitochondrial loci as might be expected during the early stages of species formation. Because the geographic distance between divergent populations is small and no obvious dispersal barriers exist in this region, we suggest the divergence might reflect ecologically driven selection mediated by environmental correlates of the depth gradient. As inferred for numerous shallow-water species, environmental gradients that parallel changes in depth may play a key role in the genesis and adaptive radiation of the deep-water fauna.
Human Behavior Analysis by Means of Multimodal Context Mining

There is sufficient evidence proving the impact that negative lifestyle choices have on people’s health and wellness. Changing unhealthy behaviours requires raising people’s self-awareness and also providing healthcare experts with a thorough and continuous description of the user’s conduct. Several monitoring techniques have been proposed in the past to track users’ behaviour; however, these approaches are either subjective and prone to misreporting, such as questionnaires, or only focus on a specific component of context, such as activity counters. This work presents an innovative multimodal context mining framework to inspect and infer human behaviour in a more holistic fashion. The proposed approach extends beyond the state-of-the-art, since it not only explores a sole type of context, but also combines diverse levels of context in an integral manner. Namely, low-level contexts, including activities, emotions and locations, are identified from heterogeneous sensory data through machine learning techniques. Low-level contexts are combined using ontological mechanisms to derive a more abstract representation of the user’s context, here referred to as high-level context. An initial implementation of the proposed framework supporting real-time context identification is also presented. The developed system is evaluated for various realistic scenarios making use of a novel multimodal context open dataset and data on-the-go, demonstrating prominent context-aware capabilities at both low and high levels.
Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model

How ocean currents shape fungal transport, dispersal and more broadly fungal biogeography remains poorly understood. The East China Sea (ECS) is a complex and dynamic habitat with different water masses blending microbial communities. The internal transcribed spacer 2 region of fungal rDNA was analysed in water and sediment samples directly collected from the coastal (CWM), Kuroshio (KSWM), Taiwan warm (TWM) and the shelf mixed water mass (MWM), coupled with hydrographic properties measurements, to determine how ocean currents impact the fungal community composition. Almost 9k fungal operational taxonomic units (OTUs) spanning six phyla, 25 known classes, 102 orders and 694 genera were obtained. The typical terrestrial and freshwater fungal genus, Byssochlamys, was dominant in the CWM, while increasing abundance of a specific OTU affiliated with Aspergillus was revealed from coastal to open ocean water masses (TWM and KSWM). Compared with water samples, sediment harboured an increased diversity with distinct fungal communities. The proximity of the Yangtze and Qiantang estuaries homogenizes the surface water and sediment communities. A significant influence of ocean currents on community structure was found, which is believed to reduce proportionally the variation explained by environmental parameters at the scale of the total water masses. Dissolved oxygen and depth were identified as the major parameters structuring the fungal community. Our results indicate that passive fungal dispersal driven by ocean currents and river run‐off, in conjunction with the distinct hydrographic conditions of individual water masses, shapes the fungal community composition and distribution pattern in the ECS.
Effect of Coupling Agent, Methylene Diisocyanate, in the Blending of Poly(methyl methacrylate)-Modified Starch and Styrene-Butadiene Rubber

한국기술교육대학교 에너지․신소재․화학공학부접수일(2014년 2월 27일), 수정일(2014년 3월 11일), 게재확정일(2014년 3월 14일)ABSTRACTMethylene diisocyanate (MDI) was investigated as a novel interfacial modifier to enhance the performances of poly(methyl methacrylate)-modified starch/styrene-butadiene rubber (PMMA-modified starch/SBR) composites. Owing to the formation urethane linkage on one side and π-π adhesion on the other side, MDI acted as an intermediated linkage role in the PMMA-modified starch/SBR interfaces, which was evidenced by the morphological, mechanical, dynamic mechan-ical and thermal decomposition studies. As a result, the presence of MDI significantly improved the mechanical properties and thermal stability of PMMA-modified starch/SBR composites. In addition, the effect of starch concentration on the various performances of the resulted MDI/PMMA-modified starch/SBR composites, such as morphology, vulcanization characteristics, mechanical properties, toluene swelling behavior, and thermal stability were investigated and discussed in detail. The obtained MDI/PMMA-modified starch/SBR composites exhibited superior mechanical properties to carbon black/SBR (CB/SBR) compo-sites, demonstrating the potential use of the renewable starch as a substitute for CB in the rubber compounds. 요 약：메틸렌 디이소시아네이트(MDI)가 폴리(메틸 메타크릴레이트)-개질된 전분/스티렌-부타디엔 고무(PMMA- modified starch/SBR) 복합체의 물성을 향상시키기 위하여 새로운 개질제로 조사되었다. 한쪽에는 우레탄 결합의 형성 으로 인해 다른 한쪽에는 π-π 접착 때문에 MDI는 PMMA-modified starch/SBR 계면에서 중간 결합 역할을 하는 것이 형태학적, 기계적, 동역학적 그리고 열적 분해 연구에 의하여 증명되었다. 결과적으로, MDI의 존재는 PMMA-modi-fied starch/SBR 복합체의 기계적 물성과 열적 안정성을 괄목할만하게 개선하였다. 게다가, 생성된 MDI/PMMA-modified starch/SBR 복합체의 여러 가지 물성에 대한 전분 함량의 효과가 형태학, 가황 특성, 기계적 물성, 톨루엔 팽윤 거동, 그리고 열적 안정성에서 조사되었고 자세하게 논의되었다. MDI/PMMA-modified starch/SBR 복합체는 carbon black/ SBR(CB/SBR) 복합체보다 우수한 물성을 보였고, 고무 배합물에서 CB의 대체물로서 재생 가능한 전분의 유력한 사용을 보여주었다. KeywordsSBR, starch, methylene diisocyanate, interfaces
Numerical simulation of the internal flow field of a new main nozzle in an air-jet loom based on Fluent

In order to decrease the turbulence influence and the backflow during weft insertion in an air-jet loom, a new main nozzle composed of two nozzle needles connected in series is designed. The internal flow fields of the commonly used nozzle and the new nozzle are numerically studied by means of a three-dimensional model implemented by the computational fluid dynamics technique. It is observed that the turbulence strength is effectively controlled with different air supply pressures and the backflow phenomenon at the upstream passage generated by high supply pressures can be eliminated when the supply pressure is reasonably distributed into two inlets of the new nozzle. The drag force exerted on the weft yarn is calculated when the velocity distribution of the internal airflow is obtained, and results show that the drag force can be improved. Also, the numerical simulation can give some guidelines for future prototyping and experiments.
Amphotericin B Pharmacokinetics During Extracorporea/Membrane Oxygenation: A Case Report

Amphotericin B treatment during extracorporeal membrane oxygenation is at times necessary for the treatment of secondary fungemia or, less commonly, to treat a primary fungal infection. The impact of the extracorporeal circuit on the pharmacokinetics of amphotericin B have not been described in vivo. This case report describes the pharmacokinetics of amphotericin B in a patient receiving extracorporeal membrane oxygenation support for respiratory failure secondary to Blastomyces dermatitidis pneumonia. Amphotericin B concentrations were established and maintained at therapeutic levels with standard dosing despite the presence of a membrane oxygenator and intermittent replacement of extracorporeal circuit components. This suggests that no adjustments in the dosing of amphotericin B are necessary during extracorporeal membrane oxygenation.
The ATM gene in the pathogenesis of mantle-cell lymphoma.

BACKGROUND Mantle-cell lymphoma (MCL) is genetically characterized by the translocation t(11;14)(q13;q32) leading to an overexpression of cyclin-D1, but additional chromosomal abnormalities appear to be required for MCL pathogenesis. PATIENTS AND METHODS Deletions involving chromosome 11q, which were recently found as recurrent aberrations in MCL, were analyzed at the molecular level in a series of 81 MCL by fluorescence in situ hybridization (FISH) with probes from a contiguous set of yeast artificial chromosomes (YACs) spanning bands 11q14-q24. RESULTS AND CONCLUSIONS Loss of chromosome 11 material was observed in 37 of the 81 MCL cases (46%). The consensus deletion comprised YAC 801e11 containing the ATM gene. The minimal region of loss was further narrowed with P1-derived artificial chromosome (PAC) probes. This allowed the identification of a deletion confined to the genomic region of ATM, which, together with intragenic mutations found in the coding sequence, suggests a role of ATM as a tumor suppressor gene in MCL.
From nanoemulsions to self-nanoemulsions, with recent advances in self-nanoemulsifying drug delivery systems (SNEDDS)

ABSTRACT Introduction: Lipid-based drug delivery systems (LBDDS) are the most promising technique to formulate the poorly water soluble drugs. Nanotechnology strongly influences the therapeutic performance of hydrophobic drugs and has become an essential approach in drug delivery research. Self-nanoemulsifying drug delivery systems (SNEDDS) are a vital strategy that combines benefits of LBDDS and nanotechnology. SNEDDS are now preferred to improve the formulation of drugs with poor aqueous solubility. Areas covered: The review in its first part shortly describes the LBDDS, nanoemulsions and clarifies the ambiguity between nanoemulsions and microemulsions. In the second part, the review discusses SNEDDS and elaborates on the current developments and modifications in this area without discussing their associated preparation techniques and excipient properties. Expert opinion: SNEDDS have exhibit the potential to increase the bioavailability of poorly water soluble drugs. The stability of SNEDDS is further increased by solidification. Controlled release and supersaturation can be achieved, and are associated with increased patient compliance and improved drug loads, respectively. Presence of biodegradable ingredients and ease of large-scale manufacturing combined with a lot of ‘drug-targeting opportunities’ give SNEDDS a clear distinction and prominence over other solubility enhancement techniques.
Kinematical Analysis of Synthetic Dynamic Signatures Using the Sigma-Lognormal Model

The kinematical information present in synthetically generated signatures is analyzed using the Sigma-Lognormal model and compared to the kinematical properties of real samples. Experiments are carried out on totally independent development and test sets and show a high degree of similarity between humanly produced and artificial signatures. One particular flaw is found in the velocity profile of synthetic signatures. Two possible solutions are proposed to improve the synthetic generation method using the Kinematic Theory of rapid human movements.
Roles of Seed and Establishment Limitation in Determining Patterns of Afrotropical Tree Recruitment

Quantifying the relative importance of the multiple processes that limit recruitment may hold the key to understanding tropical tree diversity. Here we couple theoretical models with a large-scale, multi-species seed-sowing experiment to assess the degree to which seed and establishment limitation shape patterns of tropical tree seedling recruitment in a central African forest. Of five randomly selected species (Pancovia laurentii, Staudtia kamerunensis, Manilkara mabokeensis, Myrianthus arboreas, and Entandophragma utile), seedling establishment and survival were low (means of 16% and 6% at 3 and 24 months, respectively), and seedling density increased with seed augmentation. Seedling recruitment was best explained by species identity and the interaction of site-by-species, suggesting recruitment probabilities vary among species and sites, and supporting the role of niche-based mechanisms. Although seed augmentation enhanced initial seedling density, environmental filtering and post-establishment mortality strongly limited seedling recruitment. The relative importance of seed and establishment limitation changed with seed and seedling density and through time. The arrival of seeds most strongly affected local recruitment when seeds were nearly absent from a site (∼ 1 seed m2), but was also important when seeds arrived in extremely high densities, overwhelming niche-based mortality factors. The strength of seed limitation and density-independent mortality decreased significantly over time, while density-dependent mortality showed the opposite trend. The varying strengths of seed and establishment limitation as a function of juvenile density and time emphasize the need to evaluate their roles through later stages of a tree’s life cycle.
An empirical study on the interactions between ALTO-assisted P2P overlays and ISP networks

The recently proposed Application Layer Traffic Optimization (ALTO) framework has opened up a new dimension for Internet traffic management that is complementary to the traditional application-agnostic traffic engineering (AATE) solutions currently employed by ISPs. In this paper, we investigate how ALTO-assisted Peer-to-Peer (P2P) traffic management functions interact with the underlying AATE operations, given that there may exist different application-layer policies in the P2P overlay. By considering specific P2P peer selection behaviors on top of a traffic-engineered ISP network, we conduct a performance analysis on how the application and network-layer respective performance is influenced by different policies at the P2P side. Our empirical study offers significant insight for the future design and analysis of cross-layer network engineering approaches that involve multiple autonomous optimization entities with both consistent and non-consistent policies.