Miracle-dz/UniFAR-FTUs huggingface dataset:
Skeletal myofiber VEGF is required for the exercise training-induced increase in dentate gyrus neuronal precursor cells

Exercise signals neurogenesis in the dentate gyrus of the hippocampus. This phenomenon requires vascular endothelial growth factor (VEGF) originating from outside the blood brain barrier, but no cellular source has been identified. Thus, we hypothesized that VEGF produced by skeletal myofibers plays a role in regulating hippocampal neuronal precursor cell proliferation following exercise training. This was tested in adult conditional skeletal myofiber-specific VEGF gene-ablated mice (VEGF HSA-/- ) by providing VEGF HSA-/- and non-ablated (VEGF f/f ) littermates with running wheels for 14 days. Following this training period, hippocampal cerebral blood flow (CBF) was measured by functional magnetic resonance imaging (fMRI) and neuronal precursor cells (BrDU+/Nestin+) were detected by immunofluorescence. The VEGF f/f trained group showed improvements in both speed and endurance capacity in acute treadmill running tests (p<0.05). The VEGF HSA-/- group did not. The number of proliferating neuronal precursor cells was increased with training in VEGF f/f (p<0.05) but not in VEGF HSA-/-mice. Endothelial cell (CD31+) number did not change in this region with exercise training or skeletal myofiber VEGF gene deletion. However, resting blood flow through the hippocampal region was lower in VEGF HSA-/- mice, both untrained and trained, than untrained VEGF f/f mice (p<0.05). An acute hypoxic challenge decreased CBF (p<0.05) in untrained VEGF f/f , untrained VEGF HSA-/- , and trained VEGF HSA-/- , but not trained VEGF f/f mice. VEGF f/f , but not VEGF HSA-/- mice, were able to acutely run on a treadmill at an intensity sufficient to increase hippocampus VEGF levels. These data suggest that VEGF expressed by skeletal myofibers may directly or indirectly regulate both hippocampal blood flow and neurogenesis. a in of on 4. Resting VEGF levels in the hippocampus by induced VEGF knockout in myofibers; 5. A bout of acute exercise increases hippocampal VEGF levels in VEGF f/f mice, but VEGF HSA-/- mice; 6. A hypoxic challenge with 10% inspired O 2 lowers cerebral blood flow in trained and untrained VEGF HSA-/- mice and trained VEGF f/f mice from normoxia.
Automatic transcription and separation of the main melody in polyphonic music signals

We propose to address the problem of melody extraction along with the monaural lead instrument and accompaniment separation problem. The first task is related to Music Information Retrieval (MIR), since it aims at indexing the audio music signals with their melody. The separation problem is related to Blind Audio Source Separation (BASS), as it aims at breaking an audio mixture into several source tracks. Leading instrument source separation and main melody extraction are addressed within a unified framework. The lead instrument is modelled thanks to a source/filter production model. Its signal is generated by two hidden states, the filter state and the source state. The proposed signal spectral model therefore explicitly uses pitches both to separate the lead instrument from the others and to transcribe the pitch sequence played by that instrument, the "main melody". This model gives rise to two alternative models, a Gaussian Scaled Mixture Model (GSMM) and the Instantaneous Mixture Model (IMM). The accompaniment is modelled with a more general spectral model. Five systems are proposed. Three systems detect the fundamental frequency sequence of the lead instrument, i.e. they estimate the main melody. A system returns a musical melody transcription and the last system separates the lead instrument from the accompaniment. The results in melody transcription and source separation are at the state of the art, as shown by our participations to international evaluation campaigns (MIREX'08, MIREX'09 and SiSEC'08). The proposed extension of previous source separation works using "MIR" knowledge is therefore a very successful combination.
Integrated public transport timetable synchronization with vehicle scheduling

ABSTRACT In public transport (PT) operations planning, timetable synchronization is a useful strategy to reduce inter-route or inter-modal passenger transfer waiting time and provide a well-connected service. This work addresses the integrated PT timetable synchronization with vehicle scheduling problem for a given PT network. A new bi-objective integer programming model is developed for the problem. The objectives are to maximize the number of simultaneous vehicle arrivals at the transfer nodes of a PT network, and to minimize the required fleet size. A novel two-stage deficit function (DF)-based method is developed to solve the mathematical model using a human–machine interactive approach. At the first stage, some existing optimizers are employed to quickly generate an initial solution. At the second stage, a DF-based graphical optimization technique is utilized to generate alternative Pareto-efficient solutions by reducing the fleet size. Numerical results demonstrate that the proposed model has the potential to be applied for large-scale real-world networks.
Performance Evaluation of the Opportunistic Spectrum Access in a Cognitive Radio Network with Imperfect Sensing

—Cognitive radio networks have emerged as a promising technology to shift the actual paradigm of spectrum scarcity by allowing the cognitive users (secondary users) to use the licensed spectrum on an opportunistic basis. A continuous-time Markov chain (CTMC) can be used to model the opportunistic spectrum access (OSA) in a cognitive radio network with imperfect sensing (false alarms and misdetections). In this paper, an analytic model is developed and the performance of the system is evaluated and the numerical results are presented in terms of capacity (average number of calls completion per time unit), blocking probability, force termination probability and spectrum utilization
An Algor ithm for Impulsive Noise Removal in Color images

Abstr act. We propose an effective algorithm for impulsive noise removal in color images. The proposed method is a two-phase scheme. In the first phase, an impulse detector is designed to identify color pixels which are likely to be contaminated by noise; in the second phase, the image is restored by using a detailpreserving regularization method that applies only to those selected noise candidates. Extensive computer simulations indicate that our proposed algorithm provides significant improvement over many of the existing filtering algorithms in suppressing impulsive noise in color images.
Nutritional value, total dry matter losses, effluent production and pollutant potential in Brachiaria brizantha cv. Paiaguás grass

The objective of the present study was to evaluate losses, production and polluting potential of the effluent, nutritional value and aerobic stability of silages of Brachiaria brizantha cv. Paiaguás grass, in different particle sizes and compaction density in silage. Three theoretical particle sizes (TTP 5; 8 and 12mm) and three compaction densities (DC 550; 600 and 650kg/m 3 ) were evaluated, distributed in a factorial design (3 x 3), with four repetitions. The highest volume of effluent was found in silages with higher compaction densities (600 and 650kg/m 3 ) and lower TTP (5 and 8mm). The highest chemical oxygen demand and biochemical oxygen demand were registered in the treatment with TTP of 5mm and higher DC (600 and 650kg/m 3 ). Greater in vitro digestibility of DM was verified in the silage chopped at 5 and 8mm. There was no break in aerobic stability for 216 hours. Silage with a low compaction density 550kg/m 3 and processing with a theoretical particle size of 12mm reduces effluent losses. In general, the nutritional value of Paiaguás grass was not influenced by the treatments. Different particle sizes and compaction density did not change the aerobic stability of silages.
Unequal access of chromosomal regions to each other in Salmonella: probing chromosome structure with phage λ integrase‐mediated long‐range rearrangements

We have investigated the fluidity of the Salmonella chromosome architecture using the phage lambda site‐specific recombination system as a probe. We determined how chromosome position affects the extent of integrase‐mediated recombination between pairs of inversely oriented att sites at various loci. We also investigated the accessibility of each chromosomal att site to an extrachromosomal partner carried on a low‐copy plasmid. Recombination events were assayed by semi‐quantitative polymerase chain reaction of the attP product. The extent of recombination between the chromosome and the plasmid was generally higher than intrachromosomal recombination except for two loci, araA::attL and galT::attL, which gave no detectable recombination with any other locus. Based on 20 intervals, we found that chromosomal locations are not equally accessible to each other. Although multiple factors probably affect accessibility, the most important is the specific combination of the end‐points used. Neither the size of the intervals nor the accessibility of individual end‐points to extrachromosomal sequences is as important. These results suggest that the chromosome is not completely fluid but rather organized in some way, with barriers that limit the movement of DNA within the cell. The nature of the barriers involved in chromosomal organization remains to be determined.
BIROn - Birkbeck Institutional Research Online

This paper assesses how one large information systems (IS) organisation, Capgemini, is changing in response to the increased globalisation of software development practices. It posits the emergence of a new form of multi-national enterprise (MNE) – the heterarchy - that draws on theoretical antecedents in the field of international business. Data is gathered from two extended case studies of IS projects and the cases create new insights into the structures and behaviours of IS MNEs that are adapting to the demands of global systems development. The paper identifies four primary dimensions of impact – cultural, economic, operational and organizational – on IS MNEs and suggests how such organisations are evolving. It concludes that ‘offshoring’ may no longer be as relevant a term to describe how global IS resourcing is addressed.
WIP: Motivations and Outcomes of an Undergraduate Teaching Assistantship Program

This work in progress paper poses the research question: what are the motivations and outcomes that lead undergraduate electrical engineering students to volunteer as teaching assistants (TAs)? While graduate students have a long history of serving as TAs, the Electrical & Computer Engineering department at a large public university has replaced virtually all of their graduate teaching assistants with undergraduates. Many of this department’s courses are in the hybrid “flipped” format, wherein the in-class lecture is replaced with active learning time in which motivated teaching assistant labor can be the difference between positive and negative student experience [1]. In these courses in this department, most undergraduate TAs have been observed to volunteer many more hours than those for which they are paid. Some courses in this department have adopted the practice of having their undergraduate TAs volunteer for their first semesters before being promoted to paid positions. We present a pilot study consisting of five in-depth interviews with former undergraduate TAs, most of whom volunteered for at least one semester, from an Introduction to Signal Processing course. The data collection is ongoing; therefore, our results are not complete. Some preliminary results have been identified through multiple readings for the axes of motivation proposed by Ryan and Deci [2], whose self-determination theory states that intrinsic motivation is enhanced by feeling competent, being autonomous-supported, and having a secure relational base. Once the data set is complete, the results will help us better understand how faculty can support undergraduate TAs and build an environment that motivates them to improve engineering classrooms.
Safety and ef ﬁ cacy of manganese hydroxychloride as feed additive for all animal species EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP)

The additive under assessment, manganese hydroxychloride, contains ≥ 45% manganese (Mn). Manganese hydroxychloride is a safe source of manganese for all target species when used up to the maximum level of total manganese in complete feed authorised in the EU ( Fish 100 (total) and Other species 150 (total) mg Mn/kg feedingstuffs). Manganese hydroxychloride would substitute for other manganese sources in feed. It does not differently affect tissue deposition compared to manganese sulphate. The Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) concludes that the use of manganese hydroxychloride in animal nutrition is safe for the consumers, provided the maximum authorised manganese content in complete feed is respected. In the absence of speci ﬁ c data, the FEEDAP Panel cannot conclude on the safety for the user when handling the additive. The use of manganese hydroxychloride in animal nutrition for all animal species is not expected to pose a risk to the environment. Manganese hydroxychloride is considered a source of bioavailable manganese as indicated by a dose-dependent increase of manganese deposition in bone and liver based on two studies on chickens for fattening. The FEEDAP Panel concludes that the additive is ef ﬁ cacious in meeting the manganese requirements for all animal species/categories. any for for Lab2: / merged haematological
Zebrafishto Damaged Tissue through Blood Vessels in Gcsf-Chr19 Promotes Neutrophil Migration

G-CSF is an essential cytokine that regulates proliferation and differentiation of granulocytes from hematopoietic stem and progenitor cells. In mammals G-CSF has been identiﬁed as a key factor that promotes the release of neutrophils from the bone marrow into the blood circulation. In silico analysis indicates that zebraﬁsh has two gcsf genes, gcsf-chr12 in chromosome 12 and gcsf-chr19 in chromosome 19. Gcsf-Chr12 participates in emergency myelopoiesis, but, in contrast to its mammalian orthologue, is not involved in neutrophil migration toward damaged tissue. In turn, the function of Gcsf-Chr19 has not been examined yet. In this study, we analyzed the role of Gcsf-Chr19 in regulating neutrophil migration toward the wound. Our results indicated that during the ﬁrst h after caudal ﬁn transection, neutrophils migrate from the hematopoietic tissue toward the injury, using the extracellular matrix as a substrate. Later, between 3 and 4 h postdamage, the recruitment mainly occurs through the bloodstream, and only a few neutrophils still use the extracellular matrix to migrate. During this process, the transcriptional levels of gcsf-chr19 are considerably increased, reaching a peak 1 h postdamage. The knockdown of Gcsf-chr19 indicated that the percentage of neutrophils that reach the wound decreased after the ﬁrst h postinjury, suggesting that the knockdown speciﬁcally affects neutrophils that travel to the wound through blood vessels. Together, our data provide novel information about the regulation of neutrophil migration in zebraﬁsh, positioning Gcsf-Chr19 as a key signal during the course of an inﬂammatory process triggered by severe damage. The Journal of Immunology , 2014, 193:
Competitive Inhibition of a Set of Endoplasmic Reticulum Protein Genes (GRP78, GRP94, and ERp72) Retards Cell Growth and Lowers Viability after lonophore Treatment

GRP78, a 78-kDa protein localized in the endoplasmic reticulum (ER), has been implicated in protein processing and stress protection. Its promoter contains a 36-bp region which is conserved among GRP genes across species and has the ability to compete for trans-acting factors mediating GRP gene expression. Integration of about 800 tandem copies of this sequence into the genome of a Chinese hamster ovary cell line (DG44) results in transfectants with the following phenotypes: (i) the induction level of GRP78 by the calcium ionophore A23187 and tunicamycin is reduced 4- and 2-fold, respectively, (ii) the induction levels of two other ER luminal protein genes, GRP94 and ERp72, are simultaneously down-regulated, (iii) the growth rate of these cells is half that of transfectants without the amplified sequence, and (iv) cell viability is decreased by 25-fold after A23187 treatment. These results provide new evidence that ERp72 shares common trans-acting regulatory factors with the GRP genes and that a reduction of this set of ER proteins correlates with lower viability after ionophore treatment.
Connectivity shapes cortical thickness reductions in schizophrenia: ‘Regions that together’

Background : Cortical thickness reductions (CTRs) in schizophrenia are irregularly distributed across multiple loci. We hypothesized that cortical connectivity networks would explain the distribution of CTRs across the cortex; namely, cortico-cortical connectivity between loci with CTRs would be exceptionally strong and form an interconnected network. We tested this hypothesis in three schizophrenia cohorts: first-episode psychosis (FEP), chronic (CSZ), and treatment-resistant (TRS) schizophrenia. Methods : Structural brain images were acquired in three cross-sectional schizophrenia cohorts (FEP: n=70, CSZ: n=153, TRS: n=47) and matching healthy controls (n=54, 168 and 54, respectively). Cortical thickness was compared between the patient and respective control groups at 148 regions spanning the cortex. Structural connectivity strength between pairs of cortical regions was quantified with structural covariance analysis. Connectivity strength between CTR regions was compared to connectivity strength between 5000 sets of randomly chosen regions to establish whether CTR regions were interconnected more strongly than expected by chance. Results : Significant (FDR <.05) and widespread CTRs were found in the CSZ (79 regions) and TRS groups (106 regions), with more circumscribed CTRs in the FEP group (34 regions). CTRs with the largest effect sizes were found in frontal, temporal, cingulate, and insular regions. In all cohorts, both the patient and control groups showed significantly increased structural covariance between regions with CTRs, compared to randomly selected regions (p <.00001 all groups).
E cacy of brief dynamic interpersonal therapy in patients with major depressive disorder: a prospective, multicenter randomized controlled trial protocol

Lanlan Wang Shanghai Mental Health Center Qian Wang Beijing Anding Hospital Wenhui Jiang Shanghai Mental Health Center Jianfeng Luo Fudan University school of public health Jun Tong Wuhan Mental Health Center Xiaosi Li Anhui Mental Health Center Fang Fang Shanghai Hongkou District Mental Health Center Hongyan Wang Shanghai Mental Health Center Wenqing Zhao Shanghai Mental Health Center Diana Koszycki University of Ottawa Jianyin Qiu (  jianyin_qiu@163.com ) https://orcid.org/0000-0002-8075-2215
Validation Study of Algorithms to Identify Malignant Tumors and Serious Infections in a Japanese Administrative Healthcare Database

ABSTRACT BACKGROUND This retrospective observational study validated case-finding algorithms for malignant tumors and serious infections in a Japanese administrative healthcare database. METHODS Random samples of possible cases of each disease (January 2015–January 2018) from two hospitals participating in the Medical Data Vision Co., Ltd. (MDV) database were identified using combinations of ICD-10 diagnostic codes and other procedural/billing codes. For each disease, two physicians identified true cases among the random samples of possible cases by medical record review; a third physician made the final decision in cases where the two physicians disagreed. The accuracy of case-finding algorithms was assessed using positive predictive value (PPV) and sensitivity. RESULTS There were 2,940 possible cases of malignant tumor; 180 were randomly selected and 108 were identified as true cases after medical record review. One case-finding algorithm gave a high PPV (64.1%) without substantial loss in sensitivity (90.7%) and included ICD-10 codes for malignancy and photographing/imaging. There were 3,559 possible cases of serious infection; 200 were randomly selected and 167 were identified as true cases after medical record review. Two case-finding algorithms gave a high PPV (85.6%) with no loss in sensitivity (100%). Both case-finding algorithms included the relevant diagnostic code and immunological infection test/other related test and, of these, one also included pathological diagnosis within 1 month of hospitalization. CONCLUSIONS The case-finding algorithms in this study showed good PPV and sensitivity for identification of cases of malignant tumors and serious infections from an administrative healthcare database in Japan.
ISSN 2320-5407 International Journal of Advanced Research (2016), Volume 4, Issue 2, 636-644

Tarek K Motawi 1 , Olfat G Shaker 2 , Nancy N Shahin 1 , Hebatalla M Kamalaldin 3 , Nancy M Ahmed 4 . 1. Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt. 2. Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt. 3. Department of Internal Medicine, Faculty of Medicine, Cairo University, Cairo, Egypt. 4. Department of Biochemistry, Faculty of Pharmacy, Nahda University, Bani-Suef, Egypt.
FACTORS AFFECTING FEMALE REMATING FREQUENCY IN THE MEDITERRANEAN FRUIT FLY (DIPTERA: TEPHRITIDAE)

Mating and remating of two laboratory strains (Petapa and Guate), one wild population (An- tigua) of Ceratitis capitata (Wiedemann) and one of the hybrids between them were studied under laboratory conditions. No evidence of sexual isolation at ﬁrst mating was found among them. Remating frequency was higher under crowded conditions for the two laboratory strains. The probability of Petapa females remating depended more on the origin of the male and was negatively associated with the duration of the ﬁrst mating, but these variables had no effect on remating tendency of Guate females. Matings by Petapa males were signiﬁ- cantly less prolonged than those of Guate or hybrid males. With respect to remating, Petapa non-virgin females preferred Petapa to Guate males.
EFFECT OF DIFFERENT PLANT GROWTH REGULATORS AND ELICITORS ON SECONDARY METABOLITE PRODUCTION IN OLDENLANDIA CORYMBOSA L. (RUBIACEAE)

Oldenlandia corymbosa L. is a potential medicinal herb belongs to the family Rubiaceae. In vitro culture studies along with elicitor induced secondary metabolite production were analyzed in O. corymbosa through the present study. The nodal explants of Oldenlandia corymbosa L. were cultured on MS media supplemented with different concentrations and combinations of cytokinins and auxins and observed at regular intervals. Similarly biochemical analysis reveals that, various combinations of growth regulators along with elicitors were used to examine the occurrence of potential secondary metabolites which are present in O. corymbosa .
On the Relationship between Software Security and Energy Consumption

—Mitigating software vulnerabilities typically requires source code refactorings for implementing necessary security mechanisms. These mechanisms, although they enhance software security, they usually execute a large number of instructions, adding a performance/energy penalty to the overall application. Conversely, source code transformations are extensively performed by developers in order to improve the runtime quality of applications, in terms of performance and energy efﬁciency. These transformations may indirectly affect software security, since they may lead to the introduction of new security issues. In this work, we empirically examine the impact of source code-level energy/performance optimizations on software security and vice versa. The preliminary results of the empirical study suggest that the energy-related transformations may indirectly affect software security, whereas the incremental addition of security mechanisms may lead to an important increase in the energy consumption of software applications.