Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving efficiency of an angiotensin converting enzyme inhibitory peptide as multifunctional peptides

Bioactive peptides have been defined as specific protein fragments that have numerous biological activities. The aim of this study was to introduce three multifunctional peptides. Hence, we used rabbit lung angiotensin converting enzyme (ACE) inhibitor peptide AFKDEDTEEVPFR to prepare two analogous peptides KDEDTEEVP and KDEDTEEVH. ACE inhibitory, antioxidant, and antimicrobial activities of three synthetic peptides were investigated. Among the three peptides, KDEDTEEVP exhibited the highest ACE inhibitory activity with IC50 value of 69.63 ± 2.51 μM. Furthermore, the results of fluorescence spectroscopy and molecular modeling showed that KDEDTEEVP had more affinity to ACE than other peptides. The peptide of KDEDTEEVH showed the strongest antioxidant scavenging capacity on DPPH radicals (EC50 = 135 ± 9.62 μM), hydroxyl radicals (EC50 = 144 ± 8.73 μM), and ABTS radicals (EC50 = 62 ± 4.52%). Moreover, it showed the highest activity in iron-chelating test (EC50 = 226 ± 14.13 μM) and could also effectively inhibit the peroxidation of linoleic acid. The antimicrobial activity results showed that KDEDTEEVH had higher efficiency against Gram-positive than Gram-negative bacteria with MIC values of higher than 205 ± 10.75 μM. Although there was not a direct correlation between ACE inhibitor and antioxidant activity for analogous peptides, both analogous peptides exhibited more efficiency than the mother peptide. Thus, they can be considered as multifunctional peptides and would be beneficial ingredient to be used in food and drug industry.
Localization of an Insulin-like Growth Factor (IGF) Binding Site of Bovine IGF Binding Protein-2 Using Disulfide Mapping and Deletion Mutation Analysis of the C-terminal Domain*

We have investigated which region(s) of bovine insulin-like growth factor binding protein-2 (bIGFBP-2) interact with insulin-like growth factors (IGFs) using C-terminally truncated forms of bIGFBP-2. Initially to aid in mutant design, we defined the disulfide bonding pattern of bIGFBP-2 C-terminal region using enzymatic digestion. The pattern is Cys186-Cys220, Cys231-Cys242, and Cys244-Cys265. In addition, cyanogen bromide cleavage of bIGFBP-2 revealed that the N- and C-terminal cysteine-rich domains were not linked by disulfide bonds. Taking the disulfide bonding pattern into consideration, C-terminal truncation mutants were designed and expressed in COS-1 mammalian cells. Following IGF binding assays, a region between residues 222 and 236 was identified as important in IGF binding. Specifically, mutants truncated by 14, 36, and 48 residues from the C terminus bound IGFs to the same extent as wild type (WT) bIGFBP-2. Removal of 63 residues resulted in a greatly reduced (up to 80-fold) ability to bind IGF compared with WT bIGFBP-2. Interestingly this mutant lacked the IGF-II binding preference of WT bIGFBP-2. Residues 236–270 also appeared to play a role in determining IGF binding specificity as their removal resulted in mutants with higher IGF-II binding affinity.
Theoretical and Evolutionary Parameter Tuning of Neural Oscillators with a Double-Chain Structure for Generating Rhythmic Signals

A neural oscillator with a double-chain structure is one of the central pattern generator models used to simulate and understand rhythmic movements in living organisms. However, it is difficult to reproduce desired rhythmic signals by tuning an enormous number of parameters of neural oscillators. In this study, we propose an automatic tuning method consisting of two parts. The first involves tuning rules for both the time constants and the amplitude of the oscillatory outputs based on theoretical analyses of the relationship between parameters and outputs of the neural oscillators. The second involves an evolutionary tuning method with a two-step genetic algorithm (GA), consisting of a global GA and a local GA, for tuning parameters such as neural connection weights that have no exact tuning rule. Using numerical experiments, we confirmed that the proposed tuning method could successfully tune all parameters and generate sinusoidal waves. The tuning performance of the proposed method was less affected by factors such as the number of excitatory oscillators or the desired outputs. Furthermore, the proposed method was applied to the parameter-tuning problem of some types of artificial and biological wave reproduction and yielded optimal parameter values that generated complex rhythmic signals in Caenorhabditis elegans without trial and error.
Preparation of a three-dimensional extracellular matrix by decellularization of rabbit livers.

INTRODUCTION the availability of transplantable livers is not sufficient to fulfill the current demand for grafts, with the search for therapeutic alternatives having generated different lines of research, one of which is the use of decellularized three-dimensional biological matrices and subsequent cell seeding to obtain a functional organ. OBJECTIVE to produce a decellularization protocol from rabbit liver to generate a three-dimensional matrix. METHODS a combination of physical, chemical (Triton X-100 and SDS) and enzymatic agents to decellularize rabbit livers was used. After 68 h of retrograde perfusion, a decellularized translucent matrix was generated. To evaluate if the decellularization protocol was successful, with the extracellular matrix being preserved, we carried out histological (light microscopy and scanning electron microscopy) and biochemical (DNA quantification) studies. RESULTS the decellularization process was verified by macroscopic observation of the organ using macroscopic staining, which revealed a correct conservation of bile and vascular trees. A microscopic observation corroborated these macroscopic results, with the hematoxylin-eosin staining showing no cells or nuclear material and the presence of a portal triad. Wilde´s staining demonstrated the conservationof reticulin fibers in the decellularized matrix. In addition, scanning electron microscopy revealed a preserved Glisson´s capsule and a decellularized matrix, with the DNA quantification being less than 10 % in the decellularized liver compared to control. Finally, the time taken to develop the decellularization protocol was less than 96 hours. CONCLUSIONS the proposed decellularization protocol was correct, and was verified by an absence of cells. The hepatic matrix had preserved vascular and bile ducts with a suitable three-dimensional architecture permitting further cell seeding.
Total Ionizing Dose (TID) Effects in Extremely Scaled Ultra-Thin Channel Nanowire (NW) Gate-All-Around (GAA) InGaAs MOSFETs

InGaAs nanowire (NW) gate-all-around (GAA) MOSFETs exhibit superior radiation hardness compared to planar devices and FinFETs, benefitting from reduced gate-oxide electric fields. Applied gate bias during irradiation, channel thickness, and presence or absence of a forming gas anneal can strongly affect NW device radiation hardness. Low-frequency noise measurements are carried out to probe near-interfacial oxide-trap (border-trap) densities, and TCAD simulations are performed to assist in understanding the charge trapping in NW channel devices with high-k gate dielectrics. Optimized device structures exhibit high radiation tolerance.
Perceptions of Patients with Inflammatory Bowel Diseases on Biobanking

Background:Little is known about beliefs, understanding, and perceptions of biobanking among patients with inflammatory bowel diseases. We aimed to further understand perceptions of biobanking in the inflammatory bowel disease community. Methods:Subjects were recruited to participate in a 1:1 telephone interview on their perceptions of the risks and benefits of contributing specimens for research. These interviews informed a survey instrument evaluating perceptions of biobanking within Crohn's and Colitis Foundation of America Partners cohort. We used descriptive statistics to summarize participant responses, and bivariate statistics to compare willingness to participate in biobanking by disease and demographic factors. Results:A total of 26 interviews were conducted. Various themes emerged from the interviews and aided in the development of the survey instrument. Concerns focused on storage, loss of confidentiality, outside uses, and life insurance discrimination. A total of 1007 individuals completed the survey. Overall, 397 (39.4%) reported that they would definitely donate samples, 568 (56.4%) would probably donate, 36 (3.6%) probably not, and 6 (0.6%) would definitely not donate. No significant differences in willingness to donate samples were seen for Crohn's disease versus ulcerative colitis (P = 0.25) or for remission versus active disease (P = 0.14). For sample-type preference, 956 (89.6%) would donate blood, 997 (93.5%) saliva, and 822 (77.1%) stool. Conclusions:Majorities of patients with inflammatory bowel disease demonstrated willingness to donate specimens for biobanking, albeit with concerns. Addressing these concerns will enhance participation and engagement and create greater alignment between the desires of research participants and the governance structure and operating policies of biobanks.
Design and Validation of Real-Time Reverse Transcription-PCR Assays for Detection of Pandemic (H1N1) 2009 Virus

ABSTRACT Tracking novel influenza viruses which have the potential to cause pandemics, such as the pandemic (H1N1) 2009 virus, is a public health priority. Pandemic (H1N1) 2009 virus was first identified in Mexico in April 2009 and spread worldwide over a short period of time. Well-validated diagnostic tools that are rapid, sensitive, and specific for the detection and tracking of this virus are needed. Three real-time reverse transcription PCR (RT-PCR) assays for the amplification and detection of pandemic (H1N1) 2009 virus were developed, and their performance characteristics were compared with those of other published diagnostic assays. Thirty-nine samples confirmed to be positive for pandemic (H1N1) 2009 virus from Alberta, Canada, and six additional samples that were positive for influenza A virus but that were not typeable by using published seasonal influenza H1/H3 virus assays were available for this validation. Amplification and direct sequencing of the products was considered the “gold standard” for case identification. The new assays were sensitive and able to reproducibly detect virus in a 10−6 dilution of 4 × 106 50% tissue culture infective doses/ml when 5 μl was used as the template. They showed 100% specificity and did not cross-react with other respiratory viruses or seasonal influenza A virus subtypes. The coefficient of variation in crossing cycle threshold values for the detection of different template concentrations of pandemic (H1N1) 2009 virus was ≤3.13%, showing good reproducibility. The assays had a wide dynamic range for the detection of pandemic (H1N1) 2009 virus and utilized testing platforms appropriate for high diagnostic throughput with rapid turnaround times. We developed and validated these real-time PCR procedures with the goal that they will be useful for diagnosis and surveillance of pandemic (H1N1) 2009 virus. These findings will contribute to the informed management of this novel virus.
Hierarchical Structure And Responsibility Accounting

The literature on responsibility accounting offers two broad imperatives. First, a manager is best evaluated based on what he controls. Second, responsibility follows a hierarchical arrangement: the departmental manager is responsible for the (controllable) departmental activities, the plant manager is responsible for the activities in the various departments within the plant, the division manager is responsible for the (aggregate) activities of various plants, and so on. This literature embodies a variety of theories of behavior and organization. Examples include expectancy theory (Ronen and Livingstone [1975] and Brownell and McInnes [1968]), contingency theory (Bruns and Waterhouse [1975] and Merchant [1984]), neoclassical economics (Gordon [1964]), and principal-agent modeling (Baiman [1982]). Principal-agent modeling emphasizes information asymmetries in understanding responsibility accounting. In particular, the link between controllability and informativeness (Holmstrom [1979; 1982], Baiman and Demski [1980], and Antle and Demski [1988]) has been well explicated, and the use of relative performance evaluation (Antle and Smith [1986], Demski and Sappington [1984], and Ma, Moore, and Turnbull [1988]) has received significant attention.1 Far less attention has been afforded the hierarchical aspect of responsibility accounting. This is the focus of our analysis.
Side chain flexibility and coupling between the S4‐S5 linker and the TRP domain in thermo‐sensitive TRP channels: Insights from protein modeling

The transient receptor potential (TRP) superfamily is subdivided into several subfamilies on the basis of sequence similarity, which is highly heterogeneous but shows a molecular architecture that resembles the one present in members of the Kv channel superfamily. Because of this diversity, they produce a large variety of channels with different gating and permeability properties. Elucidation of these particular features necessarily requires comparative studies based on structural and functional data. The present study aims to compilate, analyze, and determine, in a coherent way, the relationship between intrinsic side‐chain flexibility and the allosteric coupling in members of the TRPV, TRPM, and TRPC families. Based on the recently determined structures of TRPV1 and TRPV2, we have generated protein models for single subunits of TRPV5, TRPM8, and TRPC5 channels. With these models, we focused our attention on the apparently crucial role of the GP dipeptide at the center of the S4‐S5 linker and discussed its role in the interaction with the TRP domain, specifically with the highly‐conserved Trp during this coupling. Our analysis suggests an important role of the S4‐S5L flexibility in the thermosensitivity, where heat‐activated channels possess rigid S4‐S5 linkers, whereas cold‐activated channels have flexible ones. Finally, we also present evidence of the key interaction between the conserved Trp residue of the TRP box and of several residues in the S4‐S5L, importantly the central Pro. Proteins 2017; 85:630–646. © 2016 Wiley Periodicals, Inc.
Genetic Diversity of Croatian Common Bean Landraces

In Croatia, the majority of the common bean production is based on local landraces, grown by small-scale farmers in low input production systems. Landraces are adapted to the specific growing conditions and agro-environments and show a great morphological diversity. These local landraces are in danger of genetic erosion caused by complex socio-economic changes in rural communities. The low profitability of farms and their small size, the advanced age of farmers and the replacement of traditional landraces with modern bean cultivars and/or other more profitable crops have been identified as the major factors affecting genetic erosion. Three hundred accessions belonging to most widely used landraces were evaluated by phaseolin genotyping and microsatellite marker analysis. A total of 183 different multi-locus genotypes in the panel of 300 accessions were revealed using 26 microsatellite markers. Out of 183 accessions, 27.32% were of Mesoamerican origin, 68.31% of Andean, while 4.37% of accessions represented putative hybrids between gene pools. Accessions of Andean origin were further classified into phaseolin type II (“H” or “C”) and III (“T”), the latter being more frequent. A model-based cluster analysis based on microsatellite markers revealed the presence of three clusters in congruence with the results of phaseolin type analysis.
SURVEILLANCE OF ANTIBIOTIC RESISTANCE IN CLINICAL ISOLATES OF STREPTOCOCCUS PNEUMONIAE COLLECTED IN BELGIUM DURING WINTER 2000-2001

Abstract A total of 314 isolates of Streptococcus pneumoniae collected by 10 different laboratories were tested for their susceptibility by using a microdilution technique following NCCLS recommendations. The following antibiotics were included: penicillin, ampicillin, amoxicillin, amoxicillin/clavulanate, cefaclor, cefuroxime, cefotaxime, imipenem, ciprofloxacin, gemifloxacin, levofloxacin, erythromycin, clarithromycin, azithromycin, miocamycin, clindamycin and tetracycline. The insusceptibility rate (IR) to penicillin was 21.0% [10.8% intermediate (= 0.12 - 1 μg/mL) and 10.2 % high-level (=2 μg/mL)], to cefotaxime 7.3 % [3.5 % intermediate (= 1μg/mL) and 3.8 % high-level (=2 μg/ mL)], to imipenem 3.8 % [3.8 % intermediate (= 0.25 – 0.5 μg/mL) and 0 % high-level (=1 μg/mL)], to ciprofloxacin 11.2 % [8.3 % intermediate (2 μg/mL) and 3.9 % high-level (=4 μg/mL)], to erythromycin 30.3 % [3.5 % intermediate (0.5 μg/mL) and 26.8 % high-level (=1 μg/mL)] and to tetracycline 38.5 % [0.9 % intermediate (4μg/mL) and 37.6 % high-level (=8 μg/mL)]. No decreased susceptibility was found for gemifloxacin (=0.5 μg/mL). This compound was the most active with MIC50, MIC90 and an IR of 0.015 μg/mL, 0.03 μg/mL and 0 % respectively, followed by amoxicillin/ clavulanate, amoxicillin and imipenem (MIC50, MIC90 and IR: 0.015 μg/mL, 1 μg/mL, 1.6 %/ 0.015 μg/mL, 1 μg/mL, 1.9 %/ 0.008 μg/mL, 0.12 μg/mL, 3.8 % respectively). Compared to the 1999 surveillance, penicillin and tetracycline-insusceptibility increased with 4.9 % and 15.6% respectively, while cefotaxime, erythromycin and ciprofloxacin insusceptibility decreased with 5.4 %, 5.8 % and 4.4 % respectively. MICs of all ß-lactams rose with those of penicillin for penicillin-insusceptible isolates. Imipenem, cefotaxime, amoxicillin and amoxicillin/clavulanate were generally 4, 2, 1 and 1 doubling dilutions respectively more potent than penicillin on these isolates while ampicillin, cefuroxime and cefaclor were generally 1, 2 and 4 dilutions respectively less potent. Most penicillin-insusceptible isolates remained fully susceptible to amoxicillin/clavulanate (92.4 %), amoxicillin (90.9 %) and imipenem (81.8 %). Erythromycin- tetracycline insusceptibility was the most common resistance phenotype (14.3 %). Three- and fourfold resistance was found in 12.4 %and 1.6 % respectively of the isolates. Most penicillin-insusceptible isolates were of capsular types 14 (22.7 %), 23 (21.2 %), 6 (18.2 %), 9 (13.6 %) and 19 (12.1 %).
Immunomodulatory properties of medicinal mushrooms: differential effects of water and ethanol extracts on NK cell-mediated cytotoxicity

Medicinal mushrooms have been used for centuries in Asian countries owing to their beneficial effects on health and longevity. Previous studies have reported that a single medicinal mushroom may produce both stimulatory and inhibitory effects on immune cells, depending on conditions, but the factors responsible for this apparent dichotomy remain obscure. We show here that water and ethanol extracts of cultured mycelium from various species (Agaricus blazei Murrill, Antrodia cinnamomea, Ganoderma lucidum and Hirsutella sinensis) produce opposite effects on NK cells. Water extracts enhance NK cell cytotoxic activity against cancer cells, whereas ethanol extracts inhibit cytotoxicity. Water extracts stimulate the expression and production of cytolytic proteins (perforin and granulysin) and NKG2D/NCR cell surface receptors, and activate intracellular signaling kinases (ERK, JNK and p38). In contrast, ethanol extracts inhibit expression of cytolytic and cell surface receptors. Our results suggest that the mode of extraction of medicinal mushrooms may determine the nature of the immunomodulatory effects produced on immune cells, presumably owing to the differential solubility of stimulatory and inhibitory mediators. These findings have important implications for the preparation of medicinal mushrooms to prevent and treat human diseases.
A Comparison of Local Detectors and Descriptors for Multi-Object Applications

There have been a number of evaluations and comparisons between feature detectors and descriptors and between their different implementations. These detectors and descriptors respond differently depending on the image structure. In this paper, we evaluate the overall performance of the most efficient detectors and descriptors in terms of speed and efficiency. The evaluation is carried out on a set of images of different object classes and structures with different geometric and photometric deformations. This evaluation would be useful for multi-object applications such as digilog books. It has been observed that some detectors perform better with certain object classes. Differences in performance of the descriptors vary with different image structures.
Asymmetric distribution of hypoxia-inducible factor α regulates dorsoventral axis establishment in the early sea urchin embryo

ABSTRACT Hypoxia signaling is an ancient pathway by which animals can respond to low oxygen. Malfunction of this pathway disturbs hypoxic acclimation and can result in various diseases, including cancers. The role of hypoxia signaling in early embryogenesis remains unclear. Here, we show that in the blastula of the sea urchin Strongylocentrotus purpuratus, hypoxia-inducible factor α (HIFα), the downstream transcription factor of the hypoxia pathway, is localized and transcriptionally active on the future dorsal side. This asymmetric distribution is attributable to its oxygen-sensing ability. Manipulations of the HIFα level entrained the dorsoventral axis, as the side with the higher level of HIFα tends to develop into the dorsal side. Gene expression analyses revealed that HIFα restricts the expression of nodal to the ventral side and activates several genes encoding transcription factors on the dorsal side. We also observed that intrinsic hypoxic signals in the early embryos formed a gradient, which was disrupted under hypoxic conditions. Our results reveal an unprecedented role of the hypoxia pathway in animal development. Highlighted article: Oxygen-sensitive hydroxylases regulate HIFα, and consequently nodal, asymmetry in the prospective dorsal and ventral blastula, providing positional bias for dorsoventral patterning.
[Efficacy and safety of low-energy QS Nd:YAG and QS alexandrite laser for melasma].

OBJECTIVE To assess the efficacy and safety of low-energy QS Nd : YAG and QS alexandrite laser for melsasma. METHODS We treated 32 patients with melasma using the low-energy QS Nd : YAG and QS alexandrite laser. Pigment subsided by > or = 90% was regarded as "cured", by 60% -89% as "remarkably improved", by 30% -59% as "effective", and by < 30% as "ineffective" . RESULTS Among the 32 patients, 21 patients (65.6%) were cured after (10.2 +/- 3.5) times (range: 4-15 times) of treatments, 11 patients (34.4%) were remarkably improved after (11.4 +/- 2.5) times (range: 10-14 times) of treatment. The rates of "cured" and "remarkably improved" were 81.3% and 18.7% among patients with light brown melasma and 50.0% and 50.0% among patients with dark brown melasma (P < 0.05). In patients with a disease history of less than 2 years, the rates of " cured" and "remarkably improved" were 87.5% and 12.5%, which was significantly better than the treatment results of patients with a disease history of more than 2 years (the rates of "cured" and "remarkably improved" were 58.3% and 41.7%) (P < 0.05). No hyperpigment and scarring was observed and only one patient experienced a transient pigment loss. CONCLUSIONS Lower-energy QS Nd : YAG and QS Alexandrite Laser can be used to treat patients with melasma safely and effectively. The color and disease course of melasma were factors that may affect the treatment results.
Visual servoing in medical robotics: a survey. Part I: endoscopic and direct vision imaging – techniques and applications

Intra‐operative imaging is widely used to provide visual feedback to a clinician when he/she performs a procedure. In visual servoing, surgical instruments and parts of tissue/body are tracked by processing the acquired images. This information is then used within a control loop to manoeuvre a robotic manipulator during a procedure.