Miracle-dz/UniFAR-FTUs huggingface dataset:
Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection

Polymorphic duplications in humans have been shown to contribute to phenotypic diversity. However, the evolutionary forces that maintain variable duplications across the human genome are largely unexplored. To understand the haplotypic architecture of the derived duplications, we developed a linkage-disequilibrium based method to detect insertion sites of polymorphic duplications not represented in reference genomes. This method also allows resolution of haplotypes harboring the duplications. Using this approach, we conducted genome-wide analyses and identified the insertion sites of 22 common polymorphic duplications. We found that the majority of these duplications are intrachromosomal and only one of them is an interchromosomal insertion. Further characterization of these duplications revealed significant associations to blood and skin phenotypes. Based on population genetics analyses, we found that the partial duplication of a well-characterized pigmentation-related gene, HERC2, may be selected against in European populations. We further demonstrated that the haplotype harboring the partial duplication significantly affects the expression of the HERC2P9 gene in multiple tissues. Our study sheds light onto the evolutionary impact of understudied polymorphic duplications in human populations and presents methodological insights for future studies.
Pharmacological Profile of JNJ-64179375: A Novel, Long-Acting Exosite-1 Thrombin Inhibitor

JNJ-64179375 (JNJ-9375) is a recombinant human IgG4 monoclonal antibody engineered to mimic an IgA antibody that was identified in a patient who exhibited markedly prolonged clotting times but without spontaneous bleeding episodes over several years of follow-up. The crystal structure of the JNJ-9375 antigen-binding fragment/thrombin complex showed an almost identical binding mode to that of the patient IgA. In the current study, we characterized the in vitro and in vivo properties of JNJ-9375. Surface plasmon resonance studies demonstrated that JNJ-9375 binds to α-thrombin with high affinity and specificity (KD: 0.8 nM for human thrombin). JNJ-9375 produced concentration-dependent prolongation of in vitro clotting assays in human plasma, including thrombin time (TT), ecarin clotting time, prothrombin time, and activated partial thromboplastin time, with EC2X values of 4.4, 12.4, 172.6, and 202.7 µg/ml, respectively. JNJ-9375 inhibited thrombin-induced platelet aggregation in human plasma with an IC50 value of 52.6 nM (7.8 µg/ml) and produced concentration-dependent prolongation of reaction time tested by thromboelastography. JNJ-9375 pretreatment resulted in dose-dependent reduction in thrombus formation in the rat arteriovenous (AV) shunt model of thrombosis. Robust efficacy was observed at 0.3 mg/kg accompanied by 1.5× of TT. Bleeding was increased at 3 mg/kg in a rat tail transection bleeding model demonstrating a therapeutic index of 10× compared with 1× for apixaban in the same models. Our data suggest that thrombin exosite I inhibition is efficacious against thrombosis in a pretreatment prevention animal model. SIGNIFICANCE STATEMENT JNJ-9375 is a novel, fully human monoclonal antibody that binds to the exosite I region of thrombin with high affinity and specificity. JNJ-9375 concentration dependently prolonged clotting times and inhibited thrombin-induced platelet aggregation in in vitro assays based on its mechanism of action. In an in vivo rat AV shunt model, JNJ-9375 prevented thrombus formation in a dose-dependent fashion while demonstrating reduced bleeding risk. The present study demonstrated the antithrombotic effects of inhibiting the exosite I region of thrombin when given in a prevention mode in preclinical animal models.
New Mediterranean Biodiversity Records (November 2018)

In the present article, new records are given for 18 species (6 native, 9 alien and 3 cryptogenic), belonging to 5 Phyla (i.e. Chlorophyta, Cnidaria, Annelida, Mollusca and Chordata), from 8 Mediterranean countries: Spain : A large population of Polycerella emertoni reported from the Ebro Delta, the presence of Spinimuricea klavereni is confirmed for the first time in the Catalan coast; Italy : the new record of Cryptonome turcica extends its distribution to the western Mediterranean Sea, the findings of Mawia benovici constitute the southernmost record of this species in the Adriatic Sea; Slovenia : second record of the alien seaslug Cuthona perca in the Mediterranean Sea; Montenegro : Styela plicata communities were recorded in Boka Kotorska Bay; Albania : the native great torpedo ray T etronarce nobiliana recorded for the first time in Albanian waters; Greece : first record of Lagocephalus sceleratus in the Greek side of the Adriatic, the records of Cassiopea andromeda and Pterois miles are first records of these species from the Ionian Sea, the colonial ascidians Aplidium coeruleum and Didemnum protectum are recorded for the first time in the Eastern Mediterranean, an extremely abundant population of Melibe viridis is found in Messolonghi lagoon, the record of Synchiropus sechellensis is the range expansion of this species in Greek Seas, Acetabularia caliculus is recorded for the first time from Greece; Cyprus : first records of Callionymus filamentosus and Haminoea cyanomarginata from the island; Turkey : the presence of Berthellina citrina in the Mediterranean is confirmed.
Yield of ‘Prata-Anã’ banana plants under water deficit and high plant density

Abstract Yield-improving and water-saving techniques assume great importance in the cultivation of banana plants under semiarid regions, prone to greater climate variability. The objective of this study was to evaluate yield and water-use efficiency (WUE) response of ‘Prata-Anã’ banana plants to combinations of plant densities and irrigation levels: three irrigation levels, 50, 75 and 100% crop evapotranspiration (ETc), and four plant densities, 1,666 (3.0 x 2.0 m), 2,083 (3.0 x 1.6 m), 2,666 (3.0 x 1.25 m) and 3,333 (3.0 x 1.0) plants ha-1, evaluated in two production cycles. The treatments were laid out in a randomized block design with four replicates. Increasing plant density up to 3,333 plants ha-1 induced reductions in number of leaves at harvest and some yield components; also, longer cycles, and increased yields were observed while maintaining fruit marketable size, regardless of the irrigation level used. Using an irrigation level at 50%ETc and a plant density of 3,333 plants ha-1 led to an increase in WUE of 313.92% in the first cycle and 295.27% in the second cycle compared with 1,666 plants ha-1 irrigated at 100% ETc. Higher yields and WUE can be achieved by using a plant population density of 3,333 plants ha-1 and irrigation levels below 100%ETc.
Alternatively activated NUSAP1 promotes tumor growth and indicates poor prognosis in hepatocellular carcinoma

Background Hepatocellular carcinoma (HCC) is one of the most common malignancies with high mortality. The key genes involved in initiation and development of HCC is not entirely clear. Methods We performed a meta-analysis of available transcriptome data from 6 independent HCC datasets [5 datasets from the Gene Expression Omnibus (GEO) and 1 dataset from The Cancer Genome Atlas (TCGA)]. The associations of the nucleolar and spindle-associated protein 1 (NUSAP1) expression level with clinicopathological factors and survival times were analyzed. Two representative HCC cell models were built to observe the proliferation capacity of HCC cells when NUSAP1 expression was inhibited by shNUSAP1. Results Based on the transcriptome and survival data in the GEO and TCGA databases, NUSAP1 gene was markedly upregulated in HCC. High expression of NUSAP1 in HCC is related to the iCluster1 molecular subgroup, poor survival, poor tumor differentiation and TNM stage. Additionally, pathway analysis based on RNAseq data suggested that NUSAP1 could activate the expression of genes involves in cell proliferation. Furthermore, downregulation of NUSAP1 expression could significantly inhibit the proliferation of SMMC-7721 and Huh7 cells in vitro. Conclusions Our study provides evidence that NUSAP1 may serve as a candidate prognostic marker and a target for future therapeutic intervention in HCC.
Parental investment across an altitudinal gradient in blue tits (Cyanistes caeruleus)

In this thesis, I examine parental investment and fitness in the Eurasian blue tit (Cyanistes caeruleus) in the French Pyrenees and assess potential differences due to an altitudinal gradient that creates variation in environmental "harshness". I used observational and experimental data, collected from over 500 blue tit nests. Breeding conditions are "harsher" due to colder temperatures with increasing elevation. I found that increasing altitude leads to decreased hatching success. Nevertheless, clutch size and brood mortality is comparable across the gradient. I suggest that initial reproductive decisions such as timing and amount of offspring produced heavily shape the success of a reproductive attempt. These results have implications for understanding reproductive success.
Analytical SCUC/SCED Optimization Formulation for AMES V5.0

U.S. centrally-managed wholesale power markets currently rely on Security-Constrained Unit Commitment (SCUC) and Security Constrained Economic Dispatch (SCED) optimizations to determine unit commitments, reserve, and scheduled dispatch levels for generating units during future operating periods. AMES V5.0 is an open source Java/Python platform that implements a combined SCUC/SCED optimization capturing salient features of these actual market SCUC/SCED optimizations. This report provides extensive documentation for the analytical formulation of the AMES V5.0 SCUC/SCED optimization.
A Hybrid Control Strategy of LCC-S Compensated WPT System for Wide Output Voltage and ZVS Range With Minimized Reactive Current

To regulate the output voltage of inductor–capacitor–capacitor-series (LCC-S) compensated wireless power transfer (WPT) system, a hybrid control strategy of phase shift modulation (PSM) and a switch-controlled capacitor is presented in this article. In the proposed hybrid control strategy, LCC-S compensated WPT system can realize wide output voltage regulation with zero voltage switching (ZVS), and the reactive current in a resonant tank can be minimized in the whole voltage range. Besides, the current in the primary coil of LCC-S compensated WPT system can be regulated with PSM, which helps to reduce the power loss of the primary coil at light load. Compared with conventional dual-loop hybrid control, the proposed hybrid control can regulate two control variables with one feedback loop simultaneously. To verify the theoretical analysis, a 500-W prototype with 400-V input voltage, 100−250-V output voltage is built. The experimental results show that the inverter can realize ZVS within the whole voltage range and a peak efficiency of 94.7% can be obtained.
Evaluation of resistance in response to infection of Southern corn leaf blight disease and determination of secondary metabolites produced during the interaction

In Malaysia, corn is produced in small scale due to many diseases affecting this crop and by planting susceptible hybrids. Southern corn leaf blight (SCLB) is a foliar disease caused by a fungus Cochliobolus heterostrophus. This research was aimed to evaluate resistance in selected inbred lines in response to infection of SCLB disease, and to determine the plant secondary metabolites produced during the interaction. Only one isolate (CH001) was used for this study. This isolate was identified using morphological and molecular methods, the aggressiveness of the isolate was also determined. Based on morphology and molecular results, this isolate was identified as C. heterostrophus. Pathogenicity test result showed that, the isolate was very aggressive with mean disease severity index (DSI) of 60%. Based on assessment of resistance in selected inbred lines of corn, line SLBR5 was the most resistant line with DSI mean of 20.30% at the fifth week after inoculation, line SLBS3 was the most susceptible line with DSI mean of 51.70%. The concentration of peroxidase (PO), polyphenols oxidase (PPO) and total phenolic content (TPC) were determined. In PO, resistant line SLBR5 produced higher compounds with 6320, 7600 and 5800 mgGAE/g at the 1st, 2nd and 3rd week after inoculation, respectively. Susceptible line, SLBS3 was found to produce less with 1640, 1800 and 1920 mgGAE/g at the same assessment periods. For PPO, line SLBR5 also produced higher PPO with 2440, 2560, and 2760 mgGAE/g at the 1st, 2nd and 3rd week after inoculation, respectively. Line SLBS2 produced less PPO with 1080, 1240 and 880 mgGAE/g at the same period. Similarly, in TPC, line SLBR5 produced the highest TPC with 15720, 15960 and 17720 mgGAE/g at the 1st, 2nd and 3rd week after inoculation, respectively. Line SLBS3 produced less TPC with 11960, 10240 and 10840 mgGAE/g at the same assessment periods.
Map-Based Cloning and Molecular Characterization of the Seed Dormancy 10 Locus in Rice (Oryza sativa L.)

MAP-BASED CLONING AND MOLECULAR CHARACTERIZATION OF THE SEED DORMANCY 10 LOCUS IN RICE (Oryza sativa L.) WIRAT PIPATPONGPINYO 2018 Seed dormancy is a key adaptive trait of both ecological and agricultural importance. Although many quantitative trait loci (QTL) have been associated with seed dormancy in cereal crops or model plants, a majority of them remain unknown for molecular identities and functions. Cereal crops and wild/weedy relatives usually have weak and strong seed dormancy, respectively, such as Asian cultivated rice vs. weedy rice (Oryza sativa L.). Previous research identified a set of seed dormancy QTL, including qSD10, in single plant-derived BC1F2 and BC1F3 populations from the backcross between the weedy rice line SS18-2 and the cultivated rice line EM93-1. This dissertation aimed to clone qSD10 and characterize the molecular functions of the QTL underlying gene(s). The first objective was to isolate qSD10 as a Mendelian factor and narrow its size by fine mapping to identify candidate genes. A marker-assisted singleplant-selection technique was used to advance a BC1F3 plant for three generations to synchronize the genetic background of qSD10. A population of about 4000 BC1F6 plants segregating for the qSD10-containing region was used to identify recombinants between markers on a partial high-resolution map of 3 mega bases (Mb). The recombinants were selected for marker-assisted progeny testing to delimit qSD10. Finally, qSD10 was narrowed to a genomic region of about 100 kilo bases (Kb). Physiological analysis based
Characterization of Microbiota Deteriorating Specific Coptic Manuscripts, Coptic Museum, Egypt

Manuscripts are store for knowledge that needs to be saved. In Egypt, Coptic manuscripts were subjected to plunder and deterioration movement, so from the 17 th century onwards, local authorities allowed the Copts to renovate old churches also, old manuscripts were being copied and new ones were created after the destroying and burning of old icons movements and manuscripts prevailed in 14 th -15 th centuries according to the old Christian religious and artistic traditions (Sakr et al., 2016).
Cascaded Droop and Inverse Droop Regulation for Two-Layer Coordinated Power Flow Control in Series-Connected Power Cells

To interconnect string power cells into high voltage grid in a distributed manner, a cascaded power flow regulator is proposed for simultaneous control of the injected power to the grid and flexible power sharing among string power cells. First, the traditional frequency and voltage magnitude droop control at the central controller behaves as the outer power control loop for an accurate regulation of the system power flow to main grid. Then, by setting the frequency reference and voltage magnitude reference from outer power control loop as base values for each power cells local controller, inner voltage magnitude droop for apparent power S control and the frequency inverse droop for P/E control are implemented at each power cell local controller to achieve well-decoupled real and reactive power sharing among series-connected power cells. With this control architecture, the power cells and the entire grid-tied system can obtain the flexible power regulation in a fully voltage control manner. Accordingly, seamless grid-tied to islanding operation mode transfer and power sharing of the system with other converters in autonomous islanding operation can be easily obtained.
Optimum MDC FFT Hardware Architectures in Terms of Delays and Multiplexers

In this brief, we show how to derive all the optimum multi-path delay commutator (MDC) fast Fourier transform (FFT) hardware architectures in terms of delays and multiplexers and calculate the number of such architectures. The proposed approach is based on analyzing the orders at the FFT stages that lead to optimum number of delays and multiplexers. The results show that there exist a large number of optimum MDC FFTs. This large design space can be explored in the future in order to design efficient MDC architectures that not only optimize the number of delays and multiplexers, but also other figures of merit such as the number of rotators or the input/output data order.
Lifetime-Priority-Driven Resource Allocation for WNV-Based Internet of Things

Resources allocation efficiently of wireless network virtualization (WNV) in Internet of Things (IoT) has become a key challenge owing to the conflict between the limited capacity of physical resources and the massive virtual resources requests. Focusing on time-frequency resource allocation in WNV-based IoT, this article proposes a dynamic resource allocation algorithm based on the lifetime priority (LP-DRA) of virtual network requests (VNRs). First, LP-DRA investigates the continuity of physical time-frequency resource blocks by the Karnaugh map approach, then calculates the reallocation impact factor (RIF) of existing virtual networks (VNs), and reallocates the time-frequency resources to the VN with the largest RIF. Finally, the resources are preferentially allocated to the VNs with shorter lifetimes. The performance of LP-DRA is compared with the static resource allocation algorithm and the greedy dynamic resource allocation algorithm. The simulation results show that LP-DRA can utilize physical resources more effectively, improve the acceptance rate of VNRs, and increase the revenue of the physical network.
Effect of sowing substrate on coverage and rate of weeding of directly sown annual flower beds 

The method of establishing directly sown annual flower beds has its benefits as well as problems. One of them is particularly surface weeding before sowing. The aim of the experiment was to find a solution to this problem, i.e. whether covering sowing substrates can suppress the germination and growth of weeds and improve growth parameters of annuals. The certified seed mixture of annuals and three variants of substrates that differed in ability to retain water were chosen for the experiment. Substrate A contained 70% vol. of sand and 30% vol. of peat; substrate B 50% vol. of sand, 20% vol. of siliceous marlite, 30% vol. of peat; and substrate C 30% vol. of sand, 40% vol. of siliceous marlite, 30% vol. of peat. In the control variant annuals were sown directly into the soil. The experiment was established in two different sites. Development of the mixture was monitored and evaluated all the season; the coverage with annuals and weed, the height of annuals and flowering time were evaluated. According to the results the use of sowing substrates ensured the successful development of mixtures of annuals, particularly in the initial stand development.
Does Addition of Perch Larvae as Prey Affect the Growth, Development and Cannibalism Rate of Pikeperch Larvae?

Cannibalism occurs in many cultured fish species, especially at the larval and juvenile stages of piscivorous taxa. In farmed percid species, such as pikeperch (Sander lucioperca), intra-cohort cannibalism is a major issue inducing significant losses of the initial stocking density during the first weeks of rearing. Therefore, the present study was designed to investigate the effects of perch larvae (Perca fluviatilis) as live prey on growth, survival and cannibalism in pikeperch larvae under experimental conditions. Additionally, zootechnical and behavioural variables linked to aggressiveness (S postures, attacks, bites and ingestion), and group structures were considered. The survival rate was not different between the two groups (72% with prey vs. 69% without prey), but the cannibalism rate was higher in the group with the prey (28% vs. 10%). The means of final weight and length of pikeperch larvae were higher in the group fed with perch larvae, but size heterogeneity measured by the coefficients of variation for these two parameters did not differ. The specific growth rate was higher in the group fed with perch larvae, but there was no difference between the two groups concerning Fulton’s condition factor. Among all the behavioural variables (aggressiveness, group structure), none differed between the two groups.
Vocational Teacher’s Inclination to Impart Values in Vocational Training: the Importance of Pedagogical-Didactical and Psychological Factors

The purpose of this paper was to present empirically tested model of the importance of vocational teachers’ pedagogical-didactical and psychological factors for inclination to impart their value positions in vocational education. 346 vocational teachers from 27 vocational training institutions and colleges in Lithuania completed paper-pencil questionnaires. A correlation study was designed to determine the extent to which the pedagogical-didactical and psychological determinants are related to values education. The results of Structural Equation Modelling (SEM) indicated 7 significant factors on the inclination of vocational teachers to convey values to learners in vocational education and training. Teachers’ efforts to provoke or cause emotions in students during didactical processes, as well as matching students’ practical experience and open teaching strategies were identified as the most important pedagogical-didactical factors for teacher’s inclination to impart values education. Teachers as pedagogical experts were more concerned with values education than were teachers as didactical or subject matter experts. Important psychological factors included vocational teachers’ personality traits of openness to experience and conscientiousness as well as extrinsic social motivation that were significantly related to teacher’s inclination towards values education. To our knowledge, this research is the first comprehensive attempt to evaluate the importance of pedagogical-didactical and psychological factors on the inclination of vocational teachers to convey values to learners in vocational education and training. In the future, longitudinal studies are needed to make causal inferences regarding the hypothesized relationships among the variables.