Miracle-dz/UniFAR-FTUs huggingface dataset:
Specificity of peptidases secreted by filamentous fungi

ABSTRACT Peptidases are enzymes that cleave peptide bonds, yielding proteins and peptides. Enzymes in this class also perform several other functions, regulating the activation or inactivation of target substrates via proteolysis. Owing to these functions, peptidases have been extensively used in industrial and biotechnological applications. Given their potential functions, it is important to optimize the use of these enzymes, which requires determination of the specificity of each peptidase. The peptidase specificity must be taken into account in choosing a peptidase to catalyze the available protein source within the desired application. The specificity of a peptidase defines the profile of enzyme–substrate interactions, and for this the catalytic site and the arrangement of the amino acid residues involved in peptide bond cleavage need to be known. The catalytic sites of peptidases may be composed of several subsites that interact with amino acid residues for proteolysis. Filamentous fungi produce peptidases with varying specificity, and here we provide a review of those reported to date and their potential applications.
FPGA implementation of a biological neural network based on the Hodgkin-Huxley neuron model

A set of techniques for efficient implementation of Hodgkin-Huxley-based (H-H) model of a neural network on FPGA (Field Programmable Gate Array) is presented. The central implementation challenge is H-H model complexity that puts limits on the network size and on the execution speed. However, basics of the original model cannot be compromised when effect of synaptic specifications on the network behavior is the subject of study. To solve the problem, we used computational techniques such as CORDIC (Coordinate Rotation Digital Computer) algorithm and step-by-step integration in the implementation of arithmetic circuits. In addition, we employed different techniques such as sharing resources to preserve the details of model as well as increasing the network size in addition to keeping the network execution speed close to real time while having high precision. Implementation of a two mini-columns network with 120/30 excitatory/inhibitory neurons is provided to investigate the characteristic of our method in practice. The implementation techniques provide an opportunity to construct large FPGA-based network models to investigate the effect of different neurophysiological mechanisms, like voltage-gated channels and synaptic activities, on the behavior of a neural network in an appropriate execution time. Additional to inherent properties of FPGA, like parallelism and re-configurability, our approach makes the FPGA-based system a proper candidate for study on neural control of cognitive robots and systems as well.
Light-Confining Nanoporous Anodic Alumina Microcavities by Apodized Stepwise Pulse Anodization

This study presents an innovative approach to fabricate nanoporous anodic alumina optical microcavities (NAA-μCVs) with enhanced quality factor and versatile optical properties. An apodization strategy using a logarithmic negative function is applied to a stepwise pulse anodization process in order to engineer the effective medium of NAA so that it confines light efficiently. The architecture of these light-trapping photonic crystals is composed of two highly reflecting mirrors with an asymmetrically apodized effective medium. Various anodization parameters such as the anodization time, anodization period, current density offset, and pore-widening time are systematically modified to assess their effect on the optical properties of NAA-μCVs in terms of the quality factor and position of the resonance band. We demonstrate that this fabrication approach enables the generation of NAA-μCVs with a high quality factor (∼113) and well-resolved and tunable resonance bands across the spectral regions, from UV to ne.
Labor Market Conditions at School‐Leaving: Long‐Run Effects on Marriage and Fertility

In this study, we assess the long-run impact of labor market conditions at the time of school-leaving on marriage and fertility outcomes. We draw data from the National Longitudinal Survey of Youth 1979. Our sample left school between 1976 and 1989, and we use variation in the state unemployment rate at the time of school-leaving to identify persistent effects. We find that men who left school when the state unemployment rate was high are less likely to be married and have children at age 45, but are more likely to be divorced. Women, however, are more likely to have children.
We have all of the clones, now what? Toward integrating clone analysis into software quality assessment

Cloning might seems to be an unconventional way of designing and developing software, yet it is very widely practised in industrial development. The cloning research community has made substantial progress on modeling, detecting, and analyzing software clones. Although there is continuing discussion on the real role of clones on software quality, our community may agree on the need for advancing clone management techniques. Current clone management techniques concentrate on providing editing tools that allow developers to easily inspect clone instances, track their evolution, and check change consistency. In this position paper, we argue that better clone management can be achieved by responding to the fundamental needs of industry practitioners. And the possible research directions include a software problem-oriented taxonomy of clones, and a better structured clone detection report. We believe this line of research should inspire new techniques, and reach to a much wider range of professionals from both the research and industry community.
Mutually Exclusive Distribution of IS1548 and GBSi1, an Active Group II Intron Identified in Human Isolates of Group B Streptococci

ABSTRACT The present study shows that active, self-splicing group II intron GBSi1 is located downstream of the C5a-peptidase gene,scpB, in some group B streptococcus (GBS) isolates that lack insertion sequence IS1548. IS1548 was previously reported to be often present at the scpB locus in GBS isolated in association with endocarditis. Since none of 67 GBS isolates examined, 40 of which were of serotype III, harbored both IS1548 and GBSi1, these two elements are suggested to be markers for different genetic lineages in GBS serotype III. The DNA region downstream of scpB in GBS isolates harboring either GBSi1, IS1548, or none of these mobile elements was found to encode the laminin binding protein, Lmb, which shows sequence similarities to a family of streptococcal adhesins. IS1548 is inserted 9 bp upstream of the putative promoter for lmb, while the insertion site for GBSi1 is located 88 bp further upstream. Sequences highly similar to GBSi1 exist also in Streptococcus pneumoniae. An inverted repeat sequence, with features typical of transcription terminators, was identified immediately upstream of the insertion site for the group II intron both in the GBS and S. pneumoniae sequences. This motif is suggested to constitute a target for the GBS intron as well as for rather closely related introns in Bacillus halodurans, Pseudomonas alcaligenes, andPseudomonas putida. When transcripts containing the GBSi1 intron were incubated at high concentrations of ammonium and magnesium, a major product with the expected length and sequence for the ligated exons was generated. Unlike, however, all members of group II investigated so far, the excised intron was in linear, rather than in a branched (lariat), form.
Mucosal Expression of T Cell Gene Variants Is Associated with Differential Resistance to Teladorsagia circumcincta

Resistance of sheep to the gastrointestinal nematode Teladorsagia circumcincta is a heritable characteristic. Control of parasite colonization and egg production is strongly linked to IgA antibody levels regulated by Th2 T cell activation within lymphoid tissue; and persistently-infected susceptible animals develop an inflammatory Th1/Th17 response within the abomasum that fails to control infection. Differential T cell polarization therefore is associated with parasite resistance and/or susceptibility and is controlled by a specific set of transcription factors and cytokine receptors. Transcript variants of these genes have been characterized in sheep, while in humans and mice different variants of the genes are associated with inflammatory diseases. RT-qPCR was used to quantify mucosal expression of the transcript variants of the sheep genes in trickle-infected animals with defined phenotypic traits. Genes that encode full-length GATA3 and IL17RB were shown to be significantly increased in resistant sheep that had controlled parasite infection. Expression levels of both were significantly negatively correlated with abomasal worm count (a parameter of susceptibility) and positively correlated with body weight (a parameter of resistance). These data show that polarized Th2 T cells within the abomasal mucosa play an important role in the maintenance of resistance.
OOHDM-Web: an environment for implementation of hypermedia applications in the WWW

This paper shows an environment, OOHDM-Web, that allows template driven website for applications designed using, OOHDM. We show how this environment allows direct mapping of navigation and interface constructs of OOHDM into a library of functions in the CGI scripting environment CGI-LUA, extended with the DB-LUA package. OOHDM-Web allows implementation of hypermedia applications as CGI scripts that produce dynamically generated pages, whose contents are fed from a database and integrated with pre-defined templates. The paper presents the advantages of combining the two techniques, template-driven implementations and design methods, reaping benefits of their respective stregths.
Evidence for the critical role of interleukin‐12 but not interferon‐γ in the pathogenesis of experimental colitis in mice

Background and Aims: The imbalance between helper T (Th)1/Th2 cytokines has been observed in human inflammatory bowel disease and various animal models. Because interleukin (IL)‐12 and interferon‐γ (IFN‐γ) productions are known to be a hallmark of Th1‐dominant intestinal inflammation such as 2,4,6‐trinitrobenzene sulfonic acid (TNBS)‐induced colitis, we strictly addressed the roles of IFN‐γ and IL‐12 in the development of colitis, employing knockout mice with IFN‐γ receptor (IFN‐γR) or IL‐12 p40 gene disruptions and mice administered with neutralizing monoclonal antibodies (mAbs) against IFN‐γ or IL‐12.
A new low-voltage CMOS rail-to-rail balanced output current conveyor realization

In this paper, a CMOS low-voltage second generation balanced output current conveyor (BOCCII) introduced. The BOCCII has provided an n-channel differential pairs voltage follower stage instead of complementary differential pairs to provide a rail-to-rail input/output operation. A high driving current capability ensured by using a class AB topology output stage. For the proposed BOCCII, the static power consumption is 5.22mW, the open circuit input-referred noise voltage is 5/spl mu/V//spl radic/Hz, THD is -53dB, and IM3 is -42.7dB. PSpice simulations for the new BOCCII are given using 0.35/spl mu/m CMOS technology and /spl plusmn/1V supply voltage to verify the analytical results.
Patient Awareness and Symptoms From an Incisional Hernia

Incisional hernia is a common postoperative complication following open abdominal surgery with incidence varying between 3% and 20%. 1 Approximately half of all incisional hernias are diagnosed within 1 year following surgery. In the United Kingdom alone, about 10,000 incisional hernia repairs are performed annually. Incisional hernia repairs are generally elective with emergency repair due to incarceration or strangulation constituting about 15% of repairs.1 Incisional hernia repair is not a low-risk operation and generally has relatively poor results due to chronic postoperative pain and high recurrence rates.2−3 Little has been published on patients' awareness of incisional hernia following open abdominal surgery. Moreover, there are very few publications on indications for incisional hernia repair and on the natural course of such hernias. The literature suggests that symptoms and complaints usually presented by patients include pain, discomfort, cosmetic complaints, skin problems, incarceration, strangulation, functional disability, and pulmonary dysfunction.4−6 The aim of this study was to investigate whether patients were aware that they had a hernia. In addition, we sought to determine symptoms for those who knew that they had an incisional hernia.
High Prevalence of Multidrug-Tolerant Bacteria and Associated Antimicrobial Resistance Genes Isolated from Ornamental Fish and Their Carriage Water

Background Antimicrobials are used to directly control bacterial infections in pet (ornamental) fish and are routinely added to the water these fish are shipped in to suppress the growth of potential pathogens during transport. Methodology/Principal Findings To assess the potential effects of this sustained selection pressure, 127 Aeromonas spp. isolated from warm and cold water ornamental fish species were screened for tolerance to 34 antimicrobials. Representative isolates were also examined for the presence of 54 resistance genes by a combination of miniaturized microarray and conventional PCR. Forty-seven of 94 Aeromonas spp. isolates recovered from tropical ornamental fish and their carriage water were tolerant to ≥15 antibiotics, representing seven or more different classes of antimicrobial. The quinolone and fluoroquinolone resistance gene, qnrS2, was detected at high frequency (37% tested recent isolates were positive by PCR). Class 1 integrons, IncA/C broad host range plasmids and a range of other antibiotic resistance genes, including floR, bla TEM−1, tet(A), tet(D), tet(E), qacE2, sul1, and a number of different dihydrofolate reductase and aminoglycoside transferase coding genes were also detected in carriage water samples and bacterial isolates. Conclusions These data suggest that ornamental fish and their carriage water act as a reservoir for both multi-resistant bacteria and resistance genes.
OE+IOE: A novel turn model based fault tolerant routing scheme for networks-on-chip

Network-on-chip (NoC) communication architectures are increasingly being used today to interconnect cores on chip multiprocessors (CMPs). Permanent faults in NoCs due to fabrication challenges in ultra deep submicron (UDSM) technology nodes and due to wearout have led to an increased emphasis on fault tolerant design techniques. To ensure fault tolerant communication in NoCs, several fault tolerant routing algorithms have been proposed in recent years with the goal of routing flits around faults. A majority of these algorithms are based on the turn model approach due to its simplicity and inherent freedom from deadlock. However, existing turn model based fault tolerant routing algorithms are either too restrictive in the choice of paths that flits can traverse, or are tailored to work efficiently only on very specific fault distribution patterns. In this paper, we propose a novel low overhead fault tolerant routing scheme that combines the odd-even (OE) and inverted odd-even (IOE) turn models to achieve much better fault tolerance than traditional turn model based schemes. The proposed scheme uses replication opportunistically to optimize the balance between energy overhead and arrival rate. Our experimental results indicate that the proposed OE+IOE routing scheme provides better fault tolerance than existing turn model, N-random walk, and dual virtual channel based routing schemes that have been proposed in literature.
SGR : A New Efficient Kernel for Outlier Detection in Sensor Data Minimizing Mise

In sensor network, collected data is error prone due to errors during sensors and transmission. Sometimes, the sensed data may appear to be erroneous due to large deviation from normal data distribution. Such data points termed as outliers may contain some important pattern. Outliers, if neglected as erroneous data, may result in failure to detect important phenomenon. Hence, it is necessary to not only detect such data points but analyze them further to establish the reason behind such data values. The presence of outliers may distort contained information. To ensure that the information is correctly extracted, it is necessary to identify the outliers and isolate them during knowledge extraction phase. In this paper, we propose a novel unsupervised algorithm for detecting outliers based on density by coupling two principles: first, kernel density estimation and second assigning an outlier score to each object. A new kernel function building a smoother version of density estimate is proposed. An outlier score is assigned to each object by comparing local density estimate of each object to its neighbors. The two steps provide a framework for outlier detection that can be easily applied to discover new or unusual types of outliers. Experiments performed on synthetic and real datasets suggest that the proposed approach can detect outliers precisely and achieve high recall rates which in turn demonstrate the potency of the proposed approach. Copyright © 2015 IFSA Publishing, S. L.
The relationship between calcium metabolism, insulin-like growth factor-1 and pulse pressure in normotensive, normolipidaemic and non-diabetic patients

Introduction Recent evidence suggests an interaction between bone metabolism and blood pressure (BP) regulation. The aim of our study was to evaluate endocrinological and metabolic factors related to pulse pressure (PP) in normotensive, normolipidaemic, non-smoker subjects. Material and methods We consecutively enrolled 156 adults (37 males, 119 females) in summer 2009. The BP and body mass index (BMI) were recorded, and serum samples were taken for 25-hydroxy vitamin D (25-OHD), insulin-like growth factor-1 (IGF-1), growth hormone (GH), parathormone (PTH), calcium, albumin, phosphorus, glucose, triglyceride and cholesterol levels. Results In the postmenopausal group, PP was significantly associated with age and BMI, while in premenopausal patients it was inversely related to ionized calcium. In men, a reverse relationship was present between GH and IGF-1 levels and PP. Conclusions The PP was predicted by different parameters in different genders and these predictors change even in the same gender before and after menopause. Well-known predictors of PP such as age and BMI were more pronounced in postmenopausal women, but none of the groups showed a relationship between PP and 25-OHD or PTH.
Tracking for Half an Hour

Long-term tracking requires extreme stability to the multitude of model updates and robustness to the disappearance and loss of the target as such will inevitably happen. For motivation, we have taken 10 randomly selected OTB-sequences, doubled each by attaching a reversed version and repeated each double sequence 20 times. On most of these repetitive videos, the best current tracker performs worse on each loop. This illustrates the difference between optimization for short-term versus long-term tracking. In a long-term tracker a combined global and local search strategy is beneficial, allowing for recovery from failures and disappearance. Most importantly, the proposed tracker also employs cautious updating, guided by self-quality assessment. The proposed tracker is still among the best on the 20-sec OTB-videos while achieving state-of-the-art on the 100-sec UAV20L benchmark. On 10 new half-an-hour videos with city bicycling, sport games etc, the proposed tracker outperforms others by a large margin where the 2010 TLD tracker comes second.
A Feminist Perspective on Sexuality and Body Image in Females With Colorectal Cancer: An Integrative Review

Women often experience sexual dysfunction following colorectal cancer surgery. The purpose of this integrative review is to explore changes in body image and sexuality associated with colorectal cancer and its treatment in women. We used a feminist perspective to explore differences in gender role, in body image, and sexuality in the context of women who are treated for colorectal cancer. Results of our review suggest that additional studies and interventions are needed to better understand and assist women with sexual dysfunction associated with colorectal cancer. Research should focus on how age, physical, psychosocial factors influence sexual function in particular.
The superconformal gaugings in three dimensions

We show how three-dimensional superconformal theories for any number N ≤ 8 of supersymmetries can be obtained by taking a conformal limit of the corresponding three-dimensional gauged supergravity models. The superconformal theories are charac- terized by an embedding tensor that satisfies a linear and quadratic constraint. We analyze these constraints and give the general solutions for all cases. We find new N = 4,5 super- conformal theories based on the exceptional Lie superalgebras F(4), G(3) and D(2|1; α). Using the supergravity connection we discuss which massive deformations to expect. As an example we work out the details for the case of N = 6 supersymmetry.
Measurement of Indoor Wideband Millimeter Wave Wireless Channel

A frequency domain measurement around 60 GHz is described to evaluate the effectiveness of frequency diversity in mitigating the effects of multi-path fading in indoor microcellular channels. The frequency diversity for 150 MHz and other channel bandwidths to accommodate modulated signals with data rates up to 150 Mb/s is presented. Measurements are repeated under identical test conditions. The receive omni-directional antenna replaced by a directional horn to characterize the effect of the receive antenna radiation pattern on the indoor channel.
Changes in the immunohistochemical localization of the glycine receptor in the superior olivary complex of adult circling mice

Circling mice is a mutant model of spontaneous deafness exhibiting degenerated spiral ganglion cells in the cochlea and loss of organ of Corti. The balance between glycinergic inhibition and glutamatergic excitation in the lateral superior olive (LSO) is essential for the detection of inte-raural level differences. Long term weakening of glycinergic synaptic inhibition in the LSO may lead to the downregulation of synaptic release of glycine in dorsal cochlear nucleus and downregulation of postsynaptic glycine receptor (GlyR) activity in the LSO, which may contribute to hearing loss. The present study utilized an immunohistochemical method to assess changes in GlyR immunoreactivity (IR) and the cell number in the superior olivary complex (SOC) of heterozygote (+/cir) and homozygote (cir/cir) circling mice. A significant decrease in the IR was observed in all nuclei of the SOC of homozygous mice. Loss of GlyR immunoreactive cells and a decrement in cell size was also observed in the homozygotes. A decrease in the GlyR IR in the neurons and neuropils, cell number and size of the cir/cir, may lead to profound changes in inhibitory transmission and the functional properties in the SOC nuclei. Therefore, the functional loss of inhibitory neurotransmitters in the brainstem may result in deafness of adult cir/cir mice.
Long non-coding RNAs in renal cell carcinoma: A systematic review and clinical implications

Renal cell carcinoma is one of the most common malignancy in adults, its prognosis is poor in an advanced stage and early detection is difficult due to the lack of molecular biomarkers. The identification of novel biomarkers for RCC is an urgent and meaningful project. Long non-coding RNA (lncRNA) is transcribed from genomic regions with a minimum length of 200 bases and limited protein-coding potential. Recently, lncRNAs have been greatly studied in a variety of cancer types. They participate in a wide variety of biological processes including cancer biology. In this review, we provide a new insight of the profiling of lncRNAs in RCC and their roles in renal carcinogenesis, with an emphasize on their potential in diagnosis, prognosis and potential roles in RCC therapy.