Miracle-dz/UniFAR-FTUs huggingface dataset:
The BlastNP: a novel, sensitive sequence similarity searching method using overlappingly translated sequences

An alternative method to TblastX has been developed, known as blastNP. Nucleic acids in database and query sequences were translated into overlapping protein-like sequences (overlappingly translated sequences or OTSs) before searching with blastP. Thus, each nucleic acid sequence is represented by a single "protein like" sequence (instead of three hypothetical proteins in different reading frames). The BlastNP method is defined as a BlastP that is performed on an overlappingly translated nucleic acid database using a similarly converted nucleic acid query. The specificity and sensitivity of blastNP and TblastX is quantitatively very similar, except that blastNP is more sensitive to detect short sequence similarities (less than 50 residues). However, a qualitative comparison of the observed similarities showed that only 56% was detected by both methods, but 22% was indicated only by blastNP and 22% only by TblastX. For example, a statistically significant similarity between prion protein (PrP) and transcriptions factors (TF) was only detected by blastNP. A signal amplification was seen when OTS sequences were used in similarity visualisation methods (like LALIGN) instead of nucleic acids.
Improved antisense oligonucleotide induced exon skipping in the mdx mouse model of muscular dystrophy

Duchenne muscular dystrophy (DMD) is a fatal genetic disorder caused by dystrophin gene mutations that preclude synthesis of a functional protein. One potential treatment of the disorder has utilised antisense oligoribonucleotides (AOs) to induce removal of disease‐associated exons during pre‐mRNA processing. Induced in‐frame mRNA transcripts encode a shorter but functional dystrophin. We have investigated and improved the design of AOs capable of removing exon 23, and thus the disease‐causing nonsense mutation, from mRNA in the mdx mouse model of DMD.
Virtual machine scheduling for improving energy efciency in IaaS cloud

In IaaS Cloud, different mapping relationships between virtual machines (VMs) and physical machines (PMs) cause different resource utilization, so how to place VMs on PMs to reduce energy consumption is becoming one of the major concerns for cloud providers. The existing VM scheduling schemes propose optimize PMs or network resources utilization, but few of them attempt to improve the energy efficiency of these two kinds of resources simultaneously. This paper proposes a VM scheduling scheme meeting multiple resource constraints, such as the physical server size (CPU, memory, storage, bandwidth, etc.) and network link capacity to reduce both the numbers of active PMs and network elements so as to finally reduce energy consumption. Since VM scheduling problem is abstracted as a combination of bin packing problem and quadratic assignment problem, which is also known as a classic combinatorial optimization and NP-hard problem. Accordingly, we design a two-stage heuristic algorithm to solve the issue, and the simulations show that our solution outperforms the existing PM- or network-only optimization solutions.
Isolation and Characterization of Human Clonogenic Osteoblast Progenitors Immunoselected from Fetal Bone Marrow Stroma Using STRO‐1 Monoclonal Antibody

Osteoprogenitor cells present in human fetal bone marrow (BM) stroma have not been characterized. We used density gradient centrifugation, aggregation on binding lectin, and enrichment by magnetic activated cell sorting with STRO‐1 antibody to isolate STRO‐1+ cells from nonadherent human fetal BM stromal cells. Immunoselected STRO‐1+ cells were immortalized using SV‐40 large T antigen and a clone, F/STRO‐1+ A, with weak alkaline phosphatase (ALP) activity was selected. The cloned cells proliferated rapidly but were not tumorigenic. Preconfluent F/STRO‐1+ A cells showed immunoreactivity for osteopontin, α1(I) procollagen, and parathyroid hormone–related peptide, but not for the late osteoblast differentiation markers, osteocalcin (OC), or bone sialoprotein. However, differentiation of F/STRO‐1+ A cells was induced by dexamethasone and 1,25‐dihydroxyvitamin D3, as shown by increased ALP activity. In addition, osteogenesis occurred in F/STRO‐1+ A cells cultured in three‐dimentional aggregates, as assessed morphologically, histologically, and biochemically. Moreover, reverse transcription‐polymerase chain reaction analysis showed that OC expression was silent in exponentially growing cells and occurred when cell–cell contacts were established in monolayer and in aggregates, showing induction of mature osteoblast phenotype by cell–cell contacts. Thus, clonal F/STRO‐1+ A cells immunoselected from human fetal BM stroma display features of immature osteoprogenitor cells which can differentiate into mature osteogenic cells by cell–cell interactions or inducing agents. The generation by immunoselection of an immortalized clonogenic human fetal BM stroma‐derived cell line which behaves like an osteoprogenitor cell provides a novel model system for identifying the signals required for the commitment of osteoprogenitors in the human fetal BM stroma.
Achieving Flexible and Compliant Processes in Disaster Management

Workflow management systems are becoming increasingly flexible and thus open up new areas of application, such as the coordination of activities in disaster response management. However, for managing disaster events effectively, flexibility is seen as a necessary but not sufficient condition. Moreover, effective disaster management processes require comprehensive access to and the processing of public as well as private information. Since extensive data usage without adequate controls will not be accepted in any open and free society, validating compliance for flexible disaster management processes is becoming crucial for realizing the enormous options of new information and communication technologies. In this contribution, we present a novel approach for realizing adaptive controls in flexible disaster management processes.
ADVISO demonstration: a video content management system

In this demonstration we present the architecture and discuss the implementation of a video content management system called ADVISO. The system performs video segmentation and feature extraction to create an abstract representation of video. The abstracted video representation can be stored and used in a variety of applications, such as a personalized news retrieval system, home video library management and commercial detection.
Design of wideband millimeter-wave bandpass filter using substrate integrated waveguide

This paper presents the design of wideband millimeter-wave bandpass filter based on Substrate Integrated Waveguide technology. The filter is constructed by etching rectangular slots on the top metallic plane of SIW cavity. An effective lossy circuit model at mm-Wave frequencies is proposed with accurate parameters which have been extracted from full-wave electromagnetic simulations for the proposed wideband filters. As sample, two SIW filters are designed: A wideband fifth-order SIW BPF which has insertion loss of less than 1.5 dB and 28% bandwidth at a center frequency of 45GHz. The other a fourth-order BPF with less than 2Db as insertion loss and 20% bandwidth at a center frequency of 55GHz.
GRAFT-VERSUS-HOST REACTIONS IN MICE: I. KINETIC AND IMMUNOGENETIC STUDIES OF ALLOANTIGENSENSITIVE UNITS OF LYMPHOID TISSUE

SUMMARY Lymph nodes, spleen, and thymus (but not bone marrow) contain alloantigensensitive units (AASU) which proliferate in the spleens and lymph nodes of lethally irradiated, allogeneic recipient mice. Proliferation was assayed by measuring the incorporation of 5-iodo-2'-deoxyuridine-125I (125IUdR), a specific deoxyribonucleic acid (DNA) precursor. Exposure of grafted lymphoid cells to H-2 or multiple non-H-2 alloantigens was necessary to induce proliferation. Growth was exponential between 2 and 6 days after grafting, and linear relationships existed between inoculum size and 125IUdR uptake. No evidence of nonspecific stimulation of lymphoid cells or of marrowthymus cell synergism was detected. Alloantigenic stimulation enhanced generation of AASU by their immediate precursors, under conditions of limited pool size. Thymectomy prevented differentiation of AASU from marrow stem cells but did not affect formation of AASU from immediate precursors or terminal differentiation and proliferation of AASU. Mutant alleles at the W locus did not affect the growth of AASU, suggesting that separate genetic controls exist for proliferation of AASU and myelopoietic progenitor cells. However, the same immunogenetic controls affected transplantability of AASU and myelopoietic progenitor cells, since both hybrid histocompatibility (Hh-1) and modifying “resistance” genes were operating in irradiated recipients of lymph node and bone marrow cell grafts.
Effect of Consumer Ethnocentrism and Perceived Quality of Product on Buying Behavior of Domestic and Foreign Food Products: A Case Study in Pekanbaru, Riau, Indonesia

Due to the entry of foreign food products, not only domestic food products does Indonesia provide to the consumers, but also foreign food products. This study aimed to analyze the effects of consumer ethnocentrism and perceived quality product on the buying behavior of domestic and foreign food products. This study used cross-sectional design study involving data from 100 consumers of Bawah Market Pekanbaru who were chosen by convenience sampling technique. The results showed that the respondents had a medium level of consumer ethnocentrism. They perceived the quality of domestic food products higher than that of foreign food products. The results of the multinomial logistic regression test showed that ethnocentrism and perceived quality of domestic food products had a significant negative effect on the food product purchases. Specifically, consumers who had a higher level of ethnocentrism were less likely to purchase foreign food products. Meanwhile, consumers who had a higher level of perceived quality of domestic food product were less likely to purchase the mixture of domestic and foreign food products.Keywords: ethnocentrism, buying behavior, perceived quality of the product Masuknya produk makanan luar negeri ke Indonesia menyediakan konsumen alternatif bagi produk dalam negeri. Penelitian ini bertujuan untuk menganalisis pengaruh etnosentrisme konsumen dan persepsi kualitas produk terhadap perilaku pembelian produk makanan dalam dan luar negeri. Penelitian ini menggunakan desain cross sectional study dengan data yang diperoleh dari 100 orang konsumen di Pasar Bawah Pekanbaru yang dipilih menggunakan convenience sampling technique. Hasil penelitian menunjukkan etnosentrisme konsumen pada umumnya mencapai tahap sedang. Persepsi kualitas produk makanan dalam negeri lebih tinggi daripada persepsi kualitas produk makanan luar negeri. Hasil uji regresi logistik multinomial menunjukkan bahwa etnosentrisme dan persepsi kualitas produk dalam negeri memengaruhi pembelian produk makanan secara signifikan dan negatif. Konsumen yang memiliki etnosentrisme yang tinggi kurang cenderung untuk membeli produk luar negeri. Demikian juga, konsumen dengan persepsi kualitas produk dalam negeri yang tinggi kurang cenderung untuk membeli produk campuran dalam dan luar negeri.Kata kunci: etnosentrisme, persepsi kualitas produk, perilaku pembelian
Incidence of Bloodstream Infections Due to Candida Species and In Vitro Susceptibilities of Isolates Collected from 1998 to 2000 in a Population-Based Active Surveillance Program

ABSTRACT To determine the incidence of Candida bloodstream infections (BSI) and antifungal drug resistance, population-based active laboratory surveillance was conducted from October 1998 through September 2000 in two areas of the United States (Baltimore, Md., and the state of Connecticut; combined population, 4.7 million). A total of 1,143 cases were detected, for an average adjusted annual incidence of 10 per 100,000 population or 1.5 per 10,000 hospital days. In 28% of patients, Candida BSI developed prior to or on the day of admission; only 36% of patients were in an intensive care unit at the time of diagnosis. No fewer than 78% of patients had a central catheter in place at the time of diagnosis, and 50% had undergone surgery within the previous 3 months. Candida albicans comprised 45% of the isolates, followed by C. glabrata (24%), C. parapsilosis (13%), and C. tropicalis (12%). Only 1.2% of C. albicans isolates were resistant to fluconazole (MIC, ≥64 μg/ml), compared to 7% of C. glabrata isolates and 6% of C. tropicalis isolates. Only 0.9% of C. albicans isolates were resistant to itraconazole (MIC, ≥1 μg/ml), compared to 19.5% of C. glabrata isolates and 6% of C. tropicalis isolates. Only 4.3% of C. albicans isolates were resistant to flucytosine (MIC, ≥32 μg/ml), compared to <1% of C. parapsilosis and C. tropicalis isolates and no C. glabrata isolates. As determined by E-test, the MICs of amphotericin B were ≥0.38 μg/ml for 10% of Candida isolates, ≥1 μg/ml for 1.7% of isolates, and ≥2 μg/ml for 0.4% of isolates. Our findings highlight changes in the epidemiology of Candida BSI in the 1990s and provide a basis upon which to conduct further studies of selected high-risk subpopulations.
The role of regions for different forms of business organizations

Abstract The evidence for associations between area characteristics and entrepreneurship is fairly consistent in most studies. These studies, however, have disregarded the fact that the areas might be constructs that have no effect on the individual differences in entrepreneurship and, furthermore, have conflated entrepreneurship and sole proprietorship, disregarding the impact of area constructs on different forms of business organizations. Therefore, we investigate and quantify, within a multi-level framework, the importance of municipalities and regions for understanding individual differences in entrepreneurship and self employment (defined as sole proprietorship). By using register data comprising the entire Swedish population for 2000–2010, we decompose the variation for the respective form of business organization into three levels: the individual, the municipality and the region. Our results show that about 10% of the total variation in entrepreneurship can be attributed to the municipality and region level. The corresponding numbers for self employment are 3–4%. Our results indicate that regions and municipalities differ markedly in area impact for entrepreneurs compared to self employed. The results from the present study show the importance of taking into account the form of business organization in economic analysis, and they can be used when considering whether it is appropriate to focus on specific municipalities and regions for policy interventions on self-employment.
Enzymatic reaction of hydrogen peroxide-dependent peroxygenase cytochrome P450s: kinetic deuterium isotope effects and analyses by resonance Raman spectroscopy.

Cytochromes P450SP(alpha) (CYP152B1) and P450BS(beta) (CYP152A1), which are isolated from Sphingomonas paucimobilis and Bacillus subtilis, respectively, belong to the P450 superfamily, but catalyze hydroxylation reactions, in which an oxygen atom from H2O2 is efficiently introduced into fatty acids (e.g., myristic acid). P450SP(alpha) produces the alpha-hydroxylated (alpha-OH) products at 100%, while P450BS(beta) produces alpha- and beta-hydroxylated (beta-OH) products at 33 and 67%, respectively. Using deuterium-substituted fatty acids ([2,2-d2]-myristic acid and d27-myristic acid) as a substrate, the peroxygenase reactions of the two bacterial P450s were investigated. In the P450SP(alpha) reaction, we observed an intermolecular noncompetitive kinetic isotope effect on Vmax (DV = 4.1) when [2,2-d2]-myristic acid was used, suggesting that an isotopically sensitive step involving the alpha-hydrogen of the fatty acid is present in the catalytic cycle. On the other hand, D(V/K) was masked, in sharp contrast to the features of usual monooxygenases P450. The characteristic kinetic features can be interpreted in terms of the faster product formation than the substrate dissociation. A similar kinetic isotope effect was observed [DV = 4.9, D(V/K) approximately 1] for the P450BS(beta) reaction, when d27-myristic acid was used as a substrate, indicating that the reaction mechanism is the same for both peroxygenases. The resonance Raman spectral data of P450BS(beta) in the ferric and ferrous-CO forms in the presence and absence of myristic acid demonstrated that the catalytic pocket of the enzyme is polar, so that the location of the carboxylate of the substrate close to the sixth ligand of the heme could be allowed. On the basis of these results on the kinetic isotope effects and spectroscopy, we discuss the possible mechanisms of the alpha- and beta-hydroxylation of fatty acids catalyzed by peroxygenases P450SP(alpha) and P450BS(beta).
Adoption Model of Falcataria-Based Farm Forestry: A Duration Analysis Approach

Integrating perennial plant, such as Falcataria moluccana , in farming system can provide economic and environmental benefits, especially in marginal areas. Indonesian governments at all levels have been employing a number of efforts to speed-up adoption of tree planting on farm. However, the establishment of farm forestry on private land in Indonesia, especially in Java, is widely varied. While the farm forestry in some locations has been well adopted, the farmers or land users in other location are reluctant to adopt them, although the traits of farmers and farm land in both locations are similar. Most adoption studies have employed cross-sectional data in a static discrete choice modeling framework to analyze why some farmers adopt at a certain point in time. The static approach does not consider the dynamic environment in which the adoption decision is made and thus does not incorporate speed of adoption. The information of adoption speed of an innovation is important in designing extension policies as well as reengineering innovations in order to align with socio-economic conditions of the farmers. Based on data from a survey of a random sample of 117 smallholder households in Wonosobo Regency, Central Java, Indonesia, this study investigated determinants of time to adoption of farm forestry using duration analysis. Results revealed that factors that accelerate the adoption varied include age of household head, level of education of household head, off-farm employment and output price. Older farmers tend to adopt faster than the younger farmers. The other interesting findings are that off-farm employment and membership to farmers group are two most influential factors in speeding-up adoption of Falcataria -based farm forestry. The policy implications of this research are that government should design policies that promote farmers’ participation in off-farm income activities and strengthening farmer groups in addition to extension services and timber markets.
Mind the gap in university rankings: a complex network approach towards fairness

University rankings are increasingly adopted for academic comparison and success quantification, even to establish performance-based criteria for funding assignment. However, rankings are not neutral tools, and their use frequently overlooks disparities in the starting conditions of institutions. In this research, we detect and measure structural biases that affect in inhomogeneous ways the ranking outcomes of universities from diversified territorial and educational contexts. Moreover, we develop a fairer rating system based on a fully data-driven debiasing strategy that returns an equity-oriented redefinition of the achieved scores. The key idea consists in partitioning universities in similarity groups, determined from multifaceted data using complex network analysis, and referring the performance of each institution to an expectation based on its peers. Significant evidence of territorial biases emerges for official rankings concerning both the OECD and Italian university systems, hence debiasing provides relevant insights suggesting the design of fairer strategies for performance-based funding allocations.
Preventing Poststroke Depression: A 12-Week Double-Blind Randomized Treatment Trial and 21-Month Follow-up

This study examined the effect of antidepressants in preventing depression after stroke. Nondepressed poststroke patients (N = 48) were randomly assigned to receive nortriptyline, fluoxetine, or placebo for 3 months by using double-blind methodology and were followed-up for 21 months by using a naturalistic design. During the treatment period, one minor depression developed in the nortriptyline group (n = 13 at 3 months), one minor depression developed in the fluoxetine group (n = 13), and five minor depressions developed in the placebo group (n = 15;p < .05). When treatment was discontinued, nortriptyline-treated patients were more likely to develop depression and had significantly more severe depressive symptoms during the next 6 months compared with patients in the other two groups. Both nortriptyline and fluoxetine appeared to be efficacious in preventing depression after stroke. However, nortriptyline produced an increased vulnerability to depression for more than 6 months after it was discontinued. This finding suggests the need to extend prophylactic treatment and monitor patients carefully after the discontinuation of nortriptyline.
A Comprehensive Benchmark and Optimization of 5-nm Lateral and Vertical GAA 6T-SRAMs

In this paper, we present an intensive study of 6T-SRAM designs for vertical gate-all-around (GAA) transistors (VFETs) and lateral GAA transistors (LFETs) using 5-nm node design rules. Optimizations of the nanowire (NW) diameter and the gate length are also conducted to enhance the SRAM performance. Device VT retargeting has been proposed for improving the minimum operating voltage (Vmin) of SRAMs. The isoperformance and isoyield have been performed to assess and determine the benefits provided by LFET and VFET architectures, respectively. Our results show that the VFET bitcells are denser than the LFET bitcells by 20%-30%. The SRAM read stability (read static noise margin) is significantly improved using the NW channel. For a 6σ yield target and an isoarea of SRAM bitcells, Vmin of the VFET bitcell is 80 mV lower than LFET designs. Applying the proposed VT retargeting technique can allow the VFET 122 bitcell to operate at 0.57 V without using assist circuits. A standby leakage below 10 pA/cell can be achieved for both architectures. At isoperformance, the standby leakage of VFET bitcells is 2.6× lower than LFET bitcells.
The issuance of warrants in rights offerings: Agency costs and signaling effects

We examine the issuance choice across rights issues of equity, unit offerings, and standalone warrants and investigate the market reactions to these issue types. We find that agency costs, growth opportunities, and current funding needs relative to assets in place are prime drivers of the type of equity issuance choice. Managers use quality signals such as underpricing, underwriting status, and the proportion of funds raised by exercising warrants in determining the features of the warrant issue. Furthermore, we document that the market reacts more favorably to standalone warrants issues than units and equity during the rights offering period.