Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic mapping of GBE1 and its association with glycogen storage disease IV in American Quarter horses

Comparative biochemical and histopathological data suggest that a deficiency in the glycogen branching enzyme (GBE) is responsible for a fatal neonatal disease in Quarter Horse foals that closely resembles human glycogen storage disease type IV (GSD IV). Identification of DNA markers closely linked to the equine GBE1 gene would assist us in determining whether a mutation in this gene leads to the GSD IV-like condition. FISH using BAC clones as probes assigned the equine GBE1 gene to a marker deficient region of ECA26q12→q13. Four other genes, ROBO2, ROBO1, POU1F1, and HTR1F, that flank GBE1 within a 10-Mb segment of HSA3p12→p11, were tightly linked to equine GBE1 when analyzed on the Texas A&M University 5000 rad equine radiation hybrid panel, while the GLB1, MITF, RYBP, and PROS1 genes that flank this 10-Mb interval were not linked with markers in the GBE1 group. A polymorphic microsatellite (GBEms1) in a GBE1 BAC clone was then identified and genetically mapped to ECA26 on the Animal Health Trust full-sibling equine reference family. All Quarter Horse foals affected with GSD IV were homozygous for an allele of GBEms1, as well as an allele of the most closely linked microsatellite marker, while a control horse population showed significant allelic variation with these markers. This data provides strong molecular genetic support for the candidacy of the GBE1 locus in equine GSD IV.
PUBLIC OPINION IN SERBIA ON ICTY: A CHICKEN OR AN EGG?

The paper presents seven consecutive public opinion polls in Serbia (in the period 2000–2011) on the International Criminal Tribunal for the former Yugoslavia (ICTY) and its “partiality“ towards Serbs. The author connected changes in attitudes of citizens during the observed years with the public statements of the “national leaders“ about the Tribunal, as well as with the presentation of the facts of Serbian war crimes in Serbian media. Even though the observed correlation could not be interpreted in the terms of causal relation, the author pointed out to the importance of creators of the public opinion, and offered a possibility that the leading politicians and media in Serbia were not reactive to the attitudes of citizens (as they claimed) but vice versa – they created the public opinion of citizens by their statements or by presentation of the facts about Serbian war crimes.
Using Attack Information to Reduce False Positives in Network IDS

Reducing the rate of false positives is of vital importance in enhancing the usefulness of signature-based network intrusion detection systems (NIDSs). To reduce false positives, a network administrator must throughly investigate a lengthy list of signatures and carefully disable the ones that detect attacks not harmful to the user’s environment. This is a daunting task; if some signatures are disabled by mistake, the NIDS fails to detect critical remote attacks. We designed a NIDS, TrueAlarm, to reduce the rate of false positives. Conventional NIDSs alert administrators to the detection of a malicious message, regardless of whether the message actually attempts to compromise the protected server. In contrast, TrueAlarm delays the alert until it confirms that an attempt has been made. In TrueAlarm, NIDS cooperates with a server-side monitor that observes the protected server’s behavior. TrueAlarm alerts administrators only when a server-side monitor detects deviant server behavior that must have been caused by a message detected by NIDS. Our experimental results show that TrueAlarm reduces the rate of false positives. Using real network traffic collected over 15 days, TrueAlarm produced no false positives, while a conventional NIDS produced 125.
Binding orientation and specificity of calmodulin to rat olfactory cyclic nucleotide-gated ion channel

Calmodulin (CaM), the primary intracellular Ca2+ receptor, regulates a large number of key enzymes and controls a wide spectrum of important biological responses. Recognition between CaM and its target sequence in rat olfactory cyclic nucleotide-gated ion channel (OLFp) was investigated by circular dichroism (CD), fluorescence, and NMR spectroscopy. Fluorescence data showed the OLFp tightly bound to CaM with a dissociation constant of 12 nM in a 1:1 stoichiometry. Far-UV CD data showed that approximately 60% of OLFp residues formed α-helical structures when associated with CaM. NMR data showed that most of the 15N–1H HSQC cross-peaks of the 15N-labeled CaM not only shifted but also split into two sets of peaks upon association with the OLFp. Our data indicated that the two distinct CaM/OLFp complexes existed simultaneously with stable structures that were not interexchangeable within the NMR time scale. In light of the palindromic sequence of OLFp (FQRIVRLVGVIRDW) for CaM targeting, we proposed that the helical OLFp with C2 symmetry may bind to CaM in two orientations. This hypothesis is supported by the observation that only one set of 15N–1H HSQC cross-peaks of the 15N-labeled CaM was detected upon association with OLFp-M13 chimeric peptide (OLFMp), a mutated OLFp lacking the palindromic feature. The binding specificity of OLFMp to CaM was restored when the palindromic feature was destroyed. Binding modes of CaM/OLFp and CaM/OLFMp simulated by molecular docking were in accord with their distinct patterns observed in HSQC spectra. Our studies suggest that the palindromic residues in OLFp are crucial for the orientation-specific recognition by CaM.
Cognitive biometrics: a novel approach to person authentication

Biographical notes: Kenneth Revett is currently actively engaged in research focused in the development of the field of cognitive biometrics, which relies on the deployment of biosignals (EEG, ECG, EDR) for person authentication. He published the first textbook dedicated to Behavioral Biometrics (Wiley & Sons) and is currently finishing up texts in the areas of cognitive robotics, bioinformatics for computer scientists, and cognitive biometrics. He is the editor of two Inderscience journals: Int. J. of Cognitive Biometrics and the Int. J. of Cognitive Performance Support. He has authored over 130 papers (journal and conference), and served on 30+ international programme committees.
Vasopressin plus oxygen vs vasopressin alone in cirrhotic patients with portal‐hypertensive gastropathy: Effects on gastric mucosal haemodynamics and oxygenation

The effects of vasopressin plus oxygen and vasopressin alone on gastric mucosal perfusion and oxygenation were studied using reflectance spectrophotometry and laser Doppler velocimetry in 23 cirrhotic patients with portal‐hypertensive gastropathy. The measurements were performed under basal conditions and after double‐blinded administration of placebo (n= 7), vasopressin (0.3 U/min; n= 8) or vasopressin (0.3 U/min) plus nasal oxygen (4 L/min; n= 8). No significant effects on gastric mucosal haemodynamics and oxygenation were observed after placebo. In contrast, vasopressin and vasopressin plus oxygen induced a similar reduction in haemoglobin content (‐26 ± 2 and ‐21 ± 4%, respectively P < 0.01) and laser Doppler signal (‐23 ± 2 and ‐22 ± 2%, respectively, P < 0.01). Although each treatment induced a significant reduction in oxygen saturation (‐21 ± 2 and ‐7 ± 1%, respectively P < 0.01), the effect was less pronounced in patients receiving the combination than in those receiving vasopressin alone (P < 0.01). These data suggest that vasopressin and vasopressin plus oxygen reduce gastric mucosal hyperaemia and that the oxygen supplement partially protects against gastric mucosal hypoxia during vasopressin infusion in cirrhotic patients with portal‐hypertensive gastropathy.
Age-Related Relaxo-Volumetric Quantitative Magnetic Resonance Imaging of the Major Salivary Glands

Objective To study age-related characteristics of T1 and T2 relaxation times and volume of the major salivary glands. Methods Thirty-five subjects (0.5–87 years old) with normal salivary glands were imaged with mixed turbo spin-echo pulse sequences at 1.5-T magnetic resonance units. Bilateral parotid, submandibular, and sublingual glands were segmented manually. Histograms for each salivary gland were generated and modeled with Gaussian functions for every parameter. Results Seventy parotid glands, 52 submandibular glands, and 50 sublingual glands were segmented and the histograms were analyzed. The parotid gland exhibited shorter-peak T1s and longer-peak T2s relative to the submandibular and sublingual glands. The peak T2s for all glands showed a minimum value between 2 and 4 years of age and increased monotonically thereafter. From birth to early adulthood, all glands increased in size logarithmically. Conclusion Age-related relaxo-volumetric changes of the major salivary glands show clear T2 and volumetric age-related patterns for all glands.
Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis

Identification of protein translation start sites is largely a bioinformatics exercise, with relatively few confirmed by N-terminal sequencing. Translation start site determination is critical for defining both the protein sequence and the upstream DNA which may contain regulatory motifs. It is demonstrated here that translation start sites can be determined during routine protein identification, using MALDI-MS and MS/MS data to select the correct N-terminal sequence from a list of alternatives generated in silico. Applying the method to 13 proteins from Mycobacterium tuberculosis, 11 predicted translational start sites were confirmed, and two reassigned. The authors suggest that these data (be they confirmation or reassignments) are important for the annotation of both this genome and those of organisms with related genes. It was also shown that N-acetylation, reported to be rare in prokaryotes, was present in three of the 13 proteins (23 %), suggesting that in the mycobacteria this modification may be common, and an important regulator of protein function, although more proteins need to be analysed. This method can be performed with little or no additional experimental work during proteomics investigations.
An FEM study of die attach packaging effect on nanomechanical Si optical filters

This paper presents a finite element analysis of die attach packaging stress effect on emerging nanomechanical silicon optical filters. The proposed silicon optical filter is composed of Si waveguides and a microring resonator having a few hundred nm in thickness and a few tens of μm in length. Photonic integrated circuit is typically implemented by attaching a new component to a common ceramic interposer with other components. Such an attachment process would be a cause of unwanted performance deviation of MEMS or NEMS devices due to the packaging stress. Therefore, an FEM model has been used to evaluate deflection and stress of NEMS waveguides and microring resonators which are main elements for the proposed optical filter.
Scapula Free Flap for Complex Maxillofacial Reconstruction

Introduction:Composite tissue defects of the mandible and maxilla, after resection of head and neck malignancies, osteoradionecrosis, malformations, or traumas, cause functional and aesthetic problems. Nowadays, microvascular free flaps represent the main choice for the reconstruction of these defects. Among the various flaps proposed, the scapula flap has favorable characteristics that make it suitable for bone, soft tissue, or combined defects. Materials:We report 7 cases of reconstruction of complex maxillofacial defects with subscapular system flaps. The patients treated had Romberg syndrome (1 case), malignant tumors (5 cases), and result of previous trauma (1 case). Location of deficit was the maxilla (3 cases), the mandible (2 case), the ethmoidal-maxillary region (1 case) and the upper and middle thirds of the face in the last case. Methods:In 2 cases, a parascapular system flap was used; in 5 cases, a composite flap with latissimus dorsi muscle and scapular bone. Results:Neither failure of the harvested flaps nor complications in the donor site were evidenced. A good aesthetic and functional outcome was obtained in all cases. Discussion:Many free flaps have been proposed for the reconstruction of defects in the maxillofacial region such as fibula, deep circumflex iliac artery, scapula, among the bone flaps; and forearm, rectus abdominis, and anterolateral thigh, among the soft tissue flaps. The choice of the flap to use depends on the length of the bone defect and the amount of soft tissues required. The subscapular system has the advantage of providing different flaps based on the same pedicle. The osteofasciocutaneous scapular free flap, in particular, allows wide mobility of soft tissues (parascapular flap) with respect to its bone component (scapular bone), resulting suitable for defects of large size involving both the soft tissues and the bone. Conclusions:Although the fibula flap and the deep circumflex iliac artery flap remain the first choice for bone reconstructions of the mandible and maxilla, the scapula flap has some features that make its use extremely advantageous in some circumstances. In particular, we advocate the use of the osteomuscular latissimus dorsi-scapula flap for reconstruction of large-volume defects involving the bone and soft tissues, whereas fasciocutaneous parascapular flaps represent a valid alternative to forearm flap and anterolateral thigh flap in the reconstruction of soft tissue defects.
Effect of different dietary ideal protein concentrations on broiler performance

1. The aim of the study was to examine the response of male broilers of different age categories to different dietary ideal protein (IP) concentrations and to compare the effects to IP recommendations based on single lysine (Lys) requirement studies from the literature. 2. Two experiments were carried out, in which diets containing different IP concentrations (9·0 to 14·4 g apparent faecal digestible (AFD) Lys/kg) were fed to male broilers from 14 to 34 (Exp. 1) and 28 to 41 d of age (Exp. 2). The diets (12·88 MJ AMEN/kg) were prepared by the dilution technique. The effect of dietary IP concentrations on weight gain, feed intake, feed conversion efficiency (FCE) and slaughter characteristics were studied in both experiments. 3. In Exp. 1, weight gain and FCE increased linearly and fat concentration in the carcase decreased with increasing IP concentration. In Exp. 2, weight gain and FCE improved exponentially, whereas breast meat yield improved linearly with increasing dietary IP concentration. On the basis of these results, it was concluded that the weight gain and FCE of male broilers respond to higher dietary IP levels than would be expected from single lysine requirement studies in the literature.
[Immune response of Th17 cells in mesenteric lymph node of mice infected by Schistosoma japonicum].

OBJECTIVE To observe the immune response of Th17 cells in mesenteric lymph node (MLN) of C57BL/6 mice infected by Schistosoma japonicum. METHODS Twenty C57BL/6 mice were randomly divided into infected group and control group each with ten mice. The mice in infected group were infected each with 40 +/- 5 S. japonicum cercariae. Five to six weeks later, MLN lymphocytes were separated and stimulated for 4 h by anti-CD3 (1 microg/ml) and anti-CD28 (1 microg/ml) before examination of IL-17 and retinoic acid receptor-related orphan receptor gammat (ROR-gammat) mRNA by reverse transcription PCR. The level of IL-17 and IFN-gamma was detected by ELISA after culturing with supernatant for 72h. MLN lymphocytes were stimulated for 5h by 10 ng/ml phorbol myristoyl acetate (PMA) and 1 microg/ml ionomycin. The intracellular cytokines were stained and the content of Th17 and other cytokines was examined by flow cytometry. RESULTS The level of IFN-gamma [(214.3 +/- 62.6) pg/ml] and IL-17 [(176.8 +/- 62.1) pg/ml] in the supernatant of cultured MLN cells from the infected mice was significantly higher than that of normal mice [(467 +/- 13.9) and 0 pg/ml) (P < 0.05). The expression level of IL-17 and ROR-gammat mRNA was also considerably higher than that of normal mice. IL-17+ IL-4+, IL-17+ IFN-gamma+, IL-17+ IL-5+ and IL-17+ IL-9 cells accounted for 0.06%, 0.02%, 0.02%, and 0.01% of the mesenteric lymph node CD4+ T cells of the infected mice, respectively. However, IL-17+ IL-10+ and IL-17+ Foxp3+ cells were undetected. CONCLUSION The MLN of S. japonicum-infected C57BL/6 mice can induce the production of Th17 cells, and these cells can secrete IL-4, less IFN-gamma, IL-5 and IL-9, but not IL-10, and can not express Foxp3 in the infected mice.
DM‐20 mRNA Is Expressed During the Embryonic Development of the Nervous System of the Mouse

Abstract: We used both the polymerase chain reaction (PCR) and in situ hybridization to search for the presence of proteolipid protein (PLP) gene transcripts in the developing mouse. Total brain RNA extracted from 13‐19‐day embryos, analyzed by PCR, demonstrated the presence of a single transcript that was unambiguously identified with the DM‐20 mRNA. RNA samples from postnatal day 2 animals also showed a signal corresponding to the PLP transcript, in addition to the DM‐20 message. By in situ hybridization of 10‐day embryos using a DM‐20 antisense cRNA probe, we showed that the localization of the DM‐20 message was restricted to the diencephalic basal plate. On the same embryo sections, in addition to the brain localization, an intense hybridizing signal was also detected in the trigeminal and spinal ganglia, the vagal glossopharyngeal ganglion, and the sympathetic ganglion chain. The demonstration of transcription of the PLP gene, long before the beginning of the myelination process, suggests that in addition to a structural function in myelin compaction, some of the products of the PLP gene (DM‐20) may have a role during the compartmentalization and differentiation of the neural tube.
Compatible Ionic liquid‐cellulases system for hydrolysis of lignocellulosic biomass

Ionic liquids (ILs) have been increasingly recognized as novel solvents for dissolution and pretreatment of cellulose. However, cellulases are inactivated in the presence of ILs, even when present at low concentrations. To more fully exploit the benefits of ILs it is critical to develop a compatible IL‐cellulases system in which the IL is able to effectively solubilize and activate the lignocellulosic biomass, and the cellulases possess high stability and activity. In this study, we investigated the stability and activity of a commercially available cellulases mixture in the presence of different concentrations of 1‐ethyl‐3‐methylimidazolium acetate ([Emim][OAc]). A mixture of cellulases and β‐glucosidase (Celluclast1.5L, from Trichoderma reesei, and Novozyme188, from Aspergillus niger, respectively) retained 77% and 65% of its original activity after being pre‐incubated in 15% and 20% (w/v) IL solutions, respectively, at 50°C for 3 h. The cellulases mixture also retained high activity in 15% [Emim][OAc] to hydrolyze Avicel, a model substrate for cellulose analysis, with conversion efficiency of approximately 91%. Notably, the presence of different amounts of yellow poplar lignin did not interfere significantly with the enzymatic hydrolysis of Avicel. Using this IL‐cellulase system (15% [Emim][OAc]), the saccharification of yellow poplar biomass was also significantly improved (33%) compared to the untreated control (3%) during the first hour of enzymatic hydrolysis. Together, these findings provide compelling evidence that [Emim][OAc] was compatible with the cellulase mixture, and this compatible IL‐cellulases system is promising for efficient activation and hydrolysis of native biomass to produce biofuels and co‐products from the individual biomass components. Bioeng. 2011; 108:1042–1048. © 2010 Wiley Periodicals, Inc.
Prospective Analysis of Premilitary Mental Health, Somatic Symptoms, and Postdeployment Postconcussive Symptoms

Objectives Many recent studies of service members returning from deployment have focused on the health impacts of mild traumatic brain injury (mTBI), including persistent postconcussive symptoms (PCS). However, cross-sectional study designs have made it difficult to understand the role of mental health in the etiology of persistent PCS. Methods Participants were 3319 military personnel (primarily men [90%] of 25–34 years [54%]) who had completed health surveys at basic training and after deployment, on average, 4.6 years later. Negative binomial regression was used to assess the association of PCS with demographic covariates, premilitary mental health and somatic symptoms, combat experiences and mTBI during deployment, in addition to postdeployment mental health and non-PCS somatic symptoms. Results Premilitary mental health and somatic symptoms predicted PCS even when adjusting for other variables, yielding an elevated incidence rate ratio (IRR) for posttraumatic stress disorder (PTSD; IRR = 1.23, 95% confidence interval [CI] = 1.06–1.41) and somatic symptoms (mild versus minimal somatic symptoms: IRR = 1.43, 95% CI = 1.31–1.55; moderate/severe versus minimal somatic symptoms: IRR = 1.69, 95% CI = 1.43–2.06), but not for depressive symptoms. When postdeployment mental health and somatic symptom measures were added to the model, the effect of premilitary somatic symptoms remained significant. Conclusions Findings point to potential etiological contributions of premilitary characteristics, particularly a tendency to experience somatic symptoms and PTSD, as well as mTBI and combat experiences, to the development of PCS. PCS were also strongly related to concurrent postdeployment mental health.
Physiological angiogenesis is a graded, not threshold, response

The formation of new blood vessels (angiogenesis) is important during development and tissue repair. In many diseases the biggest drive for this process clearly comes from chemical signals. However, normal physiological angiogenesis, such as seen with increased muscle activity, appears to be more driven by mechanical signals including increased friction on the inside of blood vessels, and stretch of vessels caused by the surrounding muscle fibres. It is unclear whether the signals required to stimulate capillary growth act in an all‐or‐none manner. When muscles were subjected to varying degrees of stretch, angiogenesis was recruited in a graded fashion, although chemical signals were increased to a similar extent. This may prove to be important in the design of targeted therapies to alleviate problems associated with too many or too few vessels.