Miracle-dz/UniFAR-FTUs huggingface dataset:
Bayesian Unsupervised Learning of DNA Regulatory Binding Regions

Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either scan for previously known motif types or to attempt de novo identification of a fixed number (typically one) of putative motifs. Most approaches assume the existence of reliable biodatabase information to build probabilistic a priori description of the motif classes. Examples of attempts to do probabilistic unsupervised learning about the number of putative de novo motif types and their positions within a set of DNA sequences are very rare in the literature. Here we show how such a learning problem can be formulated using a Bayesian model that targets to simultaneously maximize the marginal likelihood of sequence data arising under multiple motif types as well as under the background DNA model, which equals a variable length Markov chain. It is demonstrated how the adopted Bayesian modelling strategy combined with recently introduced nonstandard stochastic computation tools yields a more tractable learning procedure than is possible with the standard Monte Carlo approaches. Improvements and extensions of the proposed approach are also discussed.
The potential of theragnostic ¹²⁴I-8H9 convection-enhanced delivery in diffuse intrinsic pontine glioma.

BACKGROUND Reasons for failure in prior human glioma convection-enhanced delivery (CED) clinical trials remain unclear. Concentration-dependent volume of distribution (Vd) measurement of CED-infused agents in the human brain is challenging and highlights a potential technical shortcoming. Activity of iodine isotope 124 ((124)I ) in tissue can be directly measured in vivo with high resolution via PET. With the potential therapeutic utility of radioimmunotherapy, we postulate (124)I conjugated to the antiglioma monoclonal antibody 8H9 may serve as a "theragnostic" agent delivered via CED to diffuse intrinsic pontine glioma. METHODS Fifteen rats underwent CED of 0.1-1.0 mCi of (131)I-8H9 to the pons for toxicity evaluation. Six additional rats underwent CED of 10 µCi of (124)I-8H9 to the pons for dosimetry, with serial microPET performed for 1 week. Two primates underwent CED of gadolinium-albumin and 1.0 mCi of (124)I-8H9 to the pons for safety and dosimetry analysis. Serial postoperative PET, blood, and CSF radioactivity counts were performed. RESULTS One rat (1.0 mCi (131)I-8H9 infusion) suffered toxicity necessitating early sacrifice. PET analysis in rats yielded a pontine absorbed dose of 37 Gy/mCi. In primates, no toxicity was observed, and absorbed pontine dose was 3.8 Gy/mCi. Activity decreased 10-fold with 48 h following CED in both animal models. Mean Vd was 0.14 cc(3) (volume of infusion [Vi] to Vd ratio = 14) in the rat and 6.2 cc(3) (Vd/Vi = 9.5) in primate. CONCLUSION The safety and feasibility of (124)I dosimetry following CED via PET is demonstrated, establishing a preclinical framework for a trial evaluating CED of (124)I-8H9 for diffuse intrinsic pontine glioma.
Prion protein glycosylation

The transmissible spongiform encephalopathies (TSE), or prion diseases are a group of transmissible neurodegenerative disorders of humans and animals. Although the infectious agent (the ‘prion’) has not yet been formally defined at the molecular level, much evidence exists to suggest that the major or sole component is an abnormal isoform of the host encoded prion protein (PrP). Different strains or isolates of the infectious agent exist, which exhibit characteristic disease phenotypes when transmitted to susceptible animals. In the absence of a nucleic acid genome it has been hard to accommodate the existence of TSE strains within the protein‐only model of prion replication. Recent work examining the conformation and glycosylation patterns of disease‐associated PrP has shown that these post‐translational modifications show strain‐specific properties and contribute to the molecular basis of TSE strain variation. This article will review the role of glycosylation in the susceptibility of cellular PrP to conversion to the disease‐associated conformation and the role of glycosylation as a marker of TSE strain type.
CURRENT PRACTICE ACROSS THE GLOBE United States and North America

Primary or delayed flexor tendon repairs in the hand have become standard practice over the past 30 years; direct end-to-end repair in the digital sheath area using a multistrand core suture (4-strand, 6-strand, or 8-strand repair) has become widely adopted over the last 10 years. Although repair methods vary, basic principles include use of strong surgical repairs, slightly higher tension over the repair site, and ensuring sufficient core suture purchase (1.0 cm). 3-0 or 4-0 sutures are used for making core sutures, and 6-0 sutures are used for peripheral suturing. A strong core suture (6-strand or greater), made with proper tension over the repair site, may circumvent the use of peripheral sutures. In the past 10 years, the policy for preservation of the pulleys has been revolutionized. A part of the A2 pulley can be incised to free tendon motion, or the entire A4 pulley may be incised to allow repair and tendon movement if other pulleys are intact. Combined active-passive motion regimes are the mainstay of postoperative care, but the details of exercise protocols vary greatly. Rubber-band traction has been almost abandoned, and purely passive motion has declined in popularity.
Identification of cowpox infection in a 13-year-old Danish boy.

developed into a pustule. He initially had systemic symptoms with high-grade fever up to 39.5oC and flu-like symptoms. At this stage he sought medical attention by an otologist who initially prescribed dicloxacillin and, when this had no effect, erythromycin, as bacterial infection was suspected. The fever abated in 4–5 days, but the neck lesion continued to enlarge and ulcerated during the second week. At the time of referral the patient presented with an indurated, indolent ulcer, 3 cm in diameter, with a hard, black eschar surrounded by erythema and local lymphadenopathy. He was treated with oral antibiotics until the viral aetiology was established and local antiseptic treatment was continued to prevent secondary infection. The lymphadenopathy gradually subsided and the ulcer healed in 6–8 weeks with some scarring. Laboratory investigations revealed a slightly raised erythrocyte sedimentation rate, while leukocyte counts, C-reactive protein and liver function tests were normal. Cutaneous anthrax and impetigo were excluded by negative swab culture from the ulcer. Swabs from the lesion were negative, as were serological tests for Bartonella henselae and Francisella tularensensis. Biopsy samples obtained for Mycobacterium tuberculosis culture were also negative. Two 4-mm punch biopsies were taken from the rim of the ulcer. Light microscopy of haematoxylin and eosin (H&E)-stained sections showed non-specific inflammatory changes in the epidermis and dermis. No cytoplasmic inclusions were seen. The swab sample was analysed initially using MagNA Pure extraction method (Total NA Isolation Kit, no. 3 038 505, Roche, Mannheim, Germany). To improve sensitivity, an additional extraction was performed subsequently, using increased sample volumes (1000 µl) combined with decreased elution volumes (50 µl). Ulcer biopsy material was split and prepared for electron microscopy and cultivation of mycobacteria, for which the latter was treated with BLL™ MycoPrep™ (BD Diagnostics, Franklin Lakes, NJ, USA) according to the manufacturer’s instructions. This material was extracted using the modified protocol.
Adrenaline and extracellular ATP switch between two modes of acid extrusion in the guinea‐pig ventricular myocyte.

1. Intracellular pH (pHi) was recorded in isolated guinea‐pig ventricular myocytes using the pH‐sensitive fluoroprobe, carboxy‐SNARF‐1 (carboxy‐seminaphthorhodafluor). 2. Addition and removal of 10 mM NH4Cl was used to induce an intracellular acid load in a myocyte perfused with HCO3(‐)‐buffered solution containing amiloride. Under these conditions, subsequent pHi recovery is known to rely upon Na(+)‐HCO3‐ co‐transport into the cell. The application of 0.5‐5 microM adrenaline resulted in an inhibition of this pHi recovery. 3. In HEPES‐buffered solution, where acid extrusion is mediated primarily by Na(+)‐H+ antiport, pHi recovery from an acid load was stimulated by the application of adrenaline. 4. In HCO3‐/CO2‐buffered solution (no amiloride), when both acid‐aquivalent extruders are activated by an intracellular acidification, adrenaline was found to slow pHi recovery. 5. When both carriers were inhibited in Na(+)‐free, HCO3(‐)‐buffered medium, adrenaline had no effect on pHi, ruling out any effect of the catecholamine on background acid loading. 6. The voltage clamp technique was used to test if the inhibitory effect of adrenaline on amiloride‐resistant, HCO3(‐)‐dependent pHi recovery was due to an efflux of HCO3‐ ions through catecholamine‐activated anion channels. During pHi recovery, membrane depolarization, sufficient to reverse the electrochemical driving force acting on HCO3‐, had no effect upon pHi recovery rate. 7. The above results show that adrenaline has direct but opposite effects on Na(+)‐HCO3‐ co‐transport and Na(+)‐H+ antiport. In the presence of this agonist, the pHi dependence of Na(+)‐HCO3‐ symport was shifted to the left along the pHi axis by 0.13 +/‐ 0.03 units (n = 4) whereas that for Na(+)‐H+ antiport was shifted in the opposite direction by only 0.07 +/‐ 0.01 units (n = 3). Following an acid load, the net effect of adrenaline under physiological conditions was, therefore, a slowing of pHi recovery. 8. The application of extracellular ATP (ATPo, 10‐50 microM) mimicked the effects of adrenaline on both Na(+)‐H+ exchange and Na(+)‐HCO3‐ symport. 9. Adenosine (50 microM) and ADP (50 microM) did not induce any inhibition of Na(+)‐HCO3‐ symport, suggesting that the inhibition induced by ATP was not mediated through P1 or P2‐purinergic receptors. 10. We conclude that Na(+)‐H+ antiport and Na(+)‐HCO3‐ symport are both coupled to adrenaline and ATPo receptors. Activation of these receptors switches acid‐equivalent extrusion from a situation dependent on both HCO3‐ and H+ ions to one nearly exclusively dependent upon H+.
Managing the Marketing/Entrepreneurship Interface in Small Knowledge‐Based Firms: A Methodological Approach

In this paper the authors address the issue of the management of the marketing/entrepreneurship interface in small entrepreneurial knowledge‐based firms (EKFs). According to the perspective presented in this work, in such firms, the management of the interface is strictly related to ensuring a suitable balance of market and technological innovation capabilities throughout each phase of firm’s life. In order to contribute to the debate in this research area, the authors propose a theoretical framework based on both organizational configuration and resource‐based theories. Within this theoretical framework, a methodology to evaluate firm’s innovation capabilities based on the use of fuzzy logic is described. The proposed methodology was tested in a field analysis whose results are presented in the paper. On the basis of these empirical results, some useful indications and practical lessons concerning the relationships between marketing/entrepreneurship and innovation in small innovative firms are discussed.
Implementation of bistcontroller for fault detection in CLB of FPGA

Today Field Programmable Gate Arrays (FPGAs) are widely used in many applications. These FPGAs are prone to different types of faults similar to other complicated integrated circuit chips. Faults may occur due to many reasons like environmental conditions or aging of the device. The rate of occurrence of permanent faults can be quite high in emerging technologies, and hence there is a need for periodic testing of such FPGAs. The Configurable Logic Blocks (CLBs) are the main logic resources for implementing sequential as well as combinatorial circuits. Built-in self-test (BIST) is a design technique that allows a circuit to test itself. It is a set of structured-test techniques for combinational and sequential logic, memories, multipliers and other embedded logic blocks. BIST controller coordinates the operations of different blocks of the BIST. BIST controller is designed to work in different modes. Here, we introduce a new approach for FPGA testing that exploits the reprogramability of an FPGA to create the BIST logic by configuring it only during off-line testing. In this way, testability is achieved without any overhead, since the BIST logic “disappears” when the circuit is reconfigured for its normal system operation. We are implementing a restartable logic BIST controller for the configurable logic blocks in Virtex-5 FPGAs by using the resources of FPGA itself. We have used XILINX ISE12.1 for simulation and synthesis.
Size-Dependent Selective Mechanisms on Males and Females and the Evolution of Sexual Size Dimorphism in Frogs

Sexual size dimorphism (SSD) varies in animals from male biased to female biased. The evolution of SSD is potentially influenced by a number of factors, such as territoriality, fecundity, and temporal breeding patterns (explosive vs. prolonged). In general, frogs show female-biased SSD with broad variance among species. Using comparative methods, we examine how different selective forces affect male and female sizes, and we test hypotheses about size-dependent mechanisms shaping SSD in frogs. Male size was weakly associated with SSD in all size classes, and we found no significant association among SSD, male size, temporal breeding pattern, and male territoriality. In contrast, female size best explained SSD variation across all size classes but especially for small-bodied species. We found a stronger evolutionary association between female body size and fecundity, and this fecundity advantage was highest in explosively breeding species. Our data indicate that the fecundity advantage associated with female body size may not be linear, such that intermediate and large females benefit less with body size increases. Therefore, size-dependent selection in females associated with fecundity and breeding patterns is an important mechanism driving SSD evolution in frogs. Our study underscores the fact that lineage-specific ecology and behavior should be incorporated in comparative analyses of animal SSD.
Single-Layered Circularly Polarized Substrate-Integrated Waveguide Horn Antenna Array

In this communication, a circularly polarized (CP) substrate-integrated waveguide horn antenna is proposed and studied. The CP horn antenna is implemented on a single-layer substrate with a thickness of $0.12\lambda _{\mathrm {\mathbf {0}}}$ at the center frequency (1.524 mm) for 24 GHz system applications. It comprises of an integrated phase controlling and power dividing structure, two waveguide antennas, and an antipodal linearly tapered slot antenna. With such a phase controlling and power dividing structure fully integrated inside the horn antenna, two orthogonal electric fields of the equal amplitude with 90° phase difference are achieved at the aperture plane of the horn antenna, thus, yielding an even effective circular polarization in a compact single-layered geometry. The measured results of the prototyped horn antenna exhibit a 5% bandwidth (23.7–24.9 GHz) with an axial ratio below 3 dB and a VSWR below 2. The gain of the antenna is around 8.5 dBi.
Concomitant Administration of Mycobacterium bovis BCG with the Meningococcal C Conjugate Vaccine to Neonatal Mice Enhances Antibody Response and Protective Efficacy

ABSTRACT Mycobacterium bovis BCG is administered to human neonates in many countries worldwide. The objective of the study was to assess if BCG could act as an adjuvant for polysaccharide-protein conjugate vaccines in newborns and thereby induce protective immunity against encapsulated bacteria in early infancy when susceptibility is high. We assessed whether BCG could enhance immune responses to a meningococcal C (MenC) conjugate vaccine, MenC-CRM197, in mice primed as neonates, broaden the antibody response from a dominant IgG1 toward a mixed IgG1 and IgG2a/IgG2b response, and increase protective efficacy, as measured by serum bactericidal activity (SBA). Two-week-old mice were primed subcutaneously (s.c.) with MenC-CRM197. BCG was administered concomitantly, a day or a week before MenC-CRM197. An adjuvant effect of BCG was observed only when it was given concomitantly with MenC-CRM197, with increased IgG response (P = 0.002) and SBA (8-fold) after a second immunization with MenC-CRM197 without BCG, indicating increased T-cell help. In neonatal mice (1 week old) primed s.c. with MenC-CRM197 together with BCG, MenC-polysaccharide (PS)-specific IgG was enhanced compared to MenC-CRM197 alone (P = 0.0015). Sixteen days after the second immunization with MenC-CRM197, increased IgG (P < 0.05), IgG1 (P < 0.05), IgG2a (P = 0.06), and IgG2b (P < 0.05) were observed, and only mice primed with MenC-CRM197 plus BCG showed affinity maturation and detectable SBA (SBA > 128). Thus, vaccination with a meningococcal conjugate vaccine (and possibly with other conjugates) may benefit from concomitant administration of BCG in the neonatal period to accelerate and enhance production of protective antibodies, compared to the current infant administration of conjugate which follows BCG vaccination at birth.
Torque Ripple Minimization of BLDC Motor with Un-Ideal Back EMF

This paper proposes a method of minimization of torque ripple of brushless dc (BLDC) motors, with un-ideal back EMF under MATLAB 7.1/Simulink environment. An idealized BLDC motor has trapezoidal back EMF waveform. However, for practical reasons like non-uniformity of magnetic material and design trade-off it is hard to produce desired trapezoidal wave shape. Therefore torque ripple appears in conventional control. In this paper, the duty cycle of the pulses is calculated in the torque controller in both normal conduction period and commutation period and in combination with a given commutation sequence fed to the inverter gates so as to minimize ripple. Moreover, the influence of finite dc supply voltage is considered in commutation period. Simulation results show that compared with conventional control, this method results in apparent reduction of torque ripple.
Effect of neck pain on verticality perception: a cohort study.

OBJECTIVE To use the Rod-and-Frame Test (RFT) as a quantification of the perception of verticality in subjects with and without neck pain. DESIGN Cohort study comparing perception of verticality in symptomatic subjects with neck pain versus a control group. SETTING Both groups were selected from 2 urban chiropractic offices treating typical neuromusculoskeletal conditions from the general community in Canada. PATIENTS Nineteen subjects (11 women, 8 men) with uncomplicated mechanical neck pain and 17 (7 women, 10 men) asymptomatic subjects. INTERVENTION The RFT offers a noninvasive method of measuring spatial orientation or the perception of verticality. Studies of the RFT indicate that performance is reliable. The RFT requires subjects to set a luminescent rod to the true vertical in the presence and absence of a luminescent background frame. MAIN OUTCOME MEASURE The amount of rotation was measured and recorded by a dial on the back of the device. RESULTS Two-way analysis of variance showed statistically significant differences in judging vertical between symptomatic and asymptomatic subjects. Unpaired t tests for each test situation and the Tukey post hoc test showed statistical differences for both groups. CONCLUSION There may be a direct connection between the structures that provide internal cues for the body's ability to sense verticality and nociceptive influences affecting the afference of these structures. The overshoot of the symptomatic group could indicate the search for additional proprioceptive information.
A soft switching boost converter using an auxiliary resonant circuit for a PV system

This paper proposes a soft switching boost converter using an auxiliary resonant circuit for a PV system. The topology is composed of a general boost converter adding an auxiliary resonant circuit which has a switch, inductor, capacitors and diode. The auxiliary resonant circuit helps the main switch operate with ZCS and ZVS. And the auxiliary switch also operates with ZVS. ZVS and ZCS techniques enable to reduce switching losses and improve the efficiency of the system. The theoretical analysis is verified through simulations and experiments. The perturbation and observation algorithm is applied for this system. Experimental results are obtained from the 1kW prototype. Efficiencies by the variable duty and load are measured through the experiment.
Desempenho fonológico de leitura e escrita em indivíduos com paralisia cerebral congênita hemiparética

Os objetivos deste estudo foram caracterizar e comparar o desempenho fonologico e de leitura e escrita em individuos com Paralisia Cerebral Hemiparetica a direita e a esquerda (PC-H). Participaram deste estudo 16 individuos com PC-H, com idade entre 7 e 13 anos, que frequentam ensino fundamental regular publico. Os individuos foram divididos em dois grupos : GSd (grupo de individuos com PC-H a direita) e GSe (grupo de individuos com PC-H a esquerda). Os resultados demonstraram que os individuos avaliados apresentam diagnostico fonaudiologico de disturbio de aprendizagem, porem, os individuos do GSe apresentaram melhor desempenho nos resultados do que os individuos do GSd no que se refere a emissao e recepcao da linguagem escrita.
Robot tcp positioning with vision - accuracy estimation of a robot visual control system

Calibrated 3D visual servoing has not fully matured as a industrial technology yet, and in order to widen its use in industrial applications its technological capability must be precisely known. Accuracy and repeatability are two of the crucial parameters in planning of any robotic task. In this paper we describe a procedure to evaluate the 2D and 3D accuracy of a robot stereo vision system consisting of two identical 1 Megapixel cameras, and present the results of the evaluation.
Frequent occurrence of gastritis and duodenitis in patients with inflammatory bowel disease

Background: The purpose was to study the epidemiology of Helicobacter‐negative gastritis among a large group of patients with inflammatory bowel disease (IBD) and healthy controls. Methods: From a computerized database of surgical pathology reports we selected 5493 patients who underwent colonoscopy and upper gastrointestinal endoscopy with biopsy results from both procedures. The presence of gastritis and duodenitis was compared among 550 case subjects with IBD and 4943 healthy control subjects. The results are expressed as prevalence rates, as well as age‐ and sex‐adjusted odds ratios with 95% confidence intervals. Results: Any type gastritis was found in 13% of controls and 25% of IBD patients (Crohn's disease [CD] 33%, ulcerative colitis [UC] 19%). Duodenitis was found in 1% of controls and 13% of IBD patients (CD 26%, UC 3%). In subjects younger than 18 years the prevalence of gastritis and duodenitis were 53% and 40% in CD, respectively, and 38% and 0% in UC, respectively. Similar prevalence rates were found in men and women. The odds ratio for Helicobacter‐negative chronic active gastritis associated with CD was 11.7 (7.5–18.0) and with UC 2.8 (1.4–5.0). The corresponding values for focally enhanced gastritis were 40.1 (15.5–114.9) in CD and 0 in UC. Conclusions: Helicobacter‐negative gastritis and duodenitis occur significantly more often in patients with IBD than healthy controls. Such upper gastrointestinal inflammation appears to be particularly common in CD and younger patients. (Inflamm Bowel Dis 2011;)