Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Rice Bran Protects against Rotavirus Diarrhea and Promotes Th1-Type Immune Responses to Human Rotavirus Vaccine in Gnotobiotic Pigs

ABSTRACT Rice bran (RB) contains a distinct stoichiometry of phytochemicals that can promote gut mucosal immune responses against enteric pathogens. The effects of RB on rotavirus diarrhea and immunogenicity of an attenuated human rotavirus (HRV) vaccine were evaluated in gnotobiotic pigs. The four treatment groups studied were RB plus vaccine, vaccine only, RB only, and mock control. Pigs in the RB groups were fed the amount of RB that replaced 10% of the pigs' total daily calorie intake from milk starting from 5 days of age until they were euthanized. Pigs in the vaccine groups were orally inoculated with two doses of the attenuated HRV vaccine. A subset of pigs from each group was orally challenged with the homologous virulent HRV on postinoculation day 28. Diarrhea and virus shedding were monitored daily from postchallenge day 0 to day 7. RB feeding significantly protected against diarrhea upon virulent HRV challenge and enhanced the protective rate of the vaccine against rotavirus diarrhea. Consistent with protection, RB significantly increased gamma interferon (IFN-γ)-producing CD4+ and CD8+ T cell responses in intestinal and systemic lymphoid tissues. Furthermore, RB also increased the number of total IgM- and IgA-secreting cells, total serum IgM, IgG, and IgA titers, and HRV-specific IgA titers in intestinal contents. RB reduced the numbers of intestinal and systemic HRV-specific IgA and IgG antibody-secreting cells and reduced serum HRV-specific IgA and IgG antibody titers before the challenge. These results demonstrate clear beneficial effects of RB in protection against rotavirus diarrhea and stimulation of nonspecific and HRV-specific immune responses, as well as its biased Th1-type adjuvant effect for the vaccine.
Free computational resources for designing selected reaction monitoring transitions

Selected reaction monitoring (SRM) is a technique for quantifying specific proteins using triple quadrupole MS. Proteins are digested into peptides and fed into MS following HPLC separation. The stream of ionized peptides is filtered by m/z ratio so only specific peptide targets enter the collision cell, where they are fragmented into product ions. A specific product ion is then filtered from the cell and its intensity measured. By spiking an isotopically labeled version of each target peptide into a sample, both native and surrogate peptides enter MS, pass the filters and transition into product ions in tandem; thus the quantity of the native peptide may be calculated by examining the relative intensities of the native and surrogate signals. The choice of precursor‐to‐product ion transitions is critical for SRM, but predicting the best candidates is challenging and time‐consuming. To alleviate this problem, software tools for designing and optimizing transitions have recently emerged, predominantly driven by data from public proteomics repositories, such as the Global Proteome Machine and PeptideAtlas. In this review, we provide an overview of the state‐of‐the‐art in automated SRM transition design tools in the public domain, explaining how the systems work and how to use them.
Systematic Review on Surgical Outcomes and Hearing Preservation for Cochlear Implantation in Children and Adults

Objective The mastoidectomy with facial recess approach (MFRA) is considered the reference standard for cochlear implantation. The suprameatal approach (SMA) was developed more recently and does not require mastoidectomy, which could influence postoperative outcomes. We aim to identify the optimal operative approach for cochlear implantation based on postoperative complications and hearing preservation in children and adults. Data Sources PubMed, EMBASE, Scopus, and Google Scholar. Review Methods Studies comparing MFRA and SMA in children and adults were eligible for inclusion. Original reports with moderate relevance and validity were included. Relevance and validity were assessed with a self-modified critical appraisal tool. This review was reported in accordance to PRISMA guidelines. Results We retrieved 294 citations. Only retrospective nonrandomized studies were identified (level III evidence). Six articles were selected for full-text inclusion and 4 articles for data extraction. No article found a significant difference between MFRA and SMA with respect to postoperative complications in children and adults. One study found a significantly (P < .023) higher pediatric MFRA mastoiditis rate; however, meta-analysis did not indicate an overall effect. Hearing preservation was reported only in adults, and outcomes between techniques did not differ. Conclusion No evidence was noted for lower complication rates or improved hearing preservation between the MFRA and SMA for cochlear implantation in children and adults. Pediatric data were available for children implanted above the age of 24 months only. Level I evidence is needed to resolve the uncertainty regarding differences in postoperative outcomes of pediatric and adult MFRA and SMA.
Surveillance of device-associated infections at a teaching hospital in rural Gujarat--India.

PURPOSE Surveillance of hospital-acquired infection (HAI), particularly device-associated infection (DAI), helps in determining the infection rates, risk factors, and in planning the preventive strategies to ensure a quality healthcare in any hospital. The present study was carried out to know the prevalence of DAI in a tertiary care teaching hospital of rural Gujarat. MATERIALS AND METHODS A prospective, site-specific surveillance of three common DAIs that is catheter-associated urinary tract infection (CA-UTI), IV-catheter-related bloodstream infection (IV-CRBSI), and ventilator-associated pneumonia (VAP) was carried out between July 2007 and April 2008, in different wards/ICUs. A surveillance plan, with guidelines and responsibilities of nurses, clinicians and microbiologist was prepared. Infection surveillance form for each patient suspected to have DAI was filled. The most representative clinical sample, depending on the type of suspected DAI, was collected using standard aseptic techniques and processed for aerobes and facultative anaerobes. All the isolates were identified and antimicrobial sensitivity testing performed as per CLSI guidelines. An accurate record of total device days for each of the indwelling devices under surveillance was also maintained. Data, collected in the prescribed formats, were analysed on monthly basis; and then, compiled at the end of the study. Descriptive analysis of the data was done and DAI rate was expressed as number of DAI per 1000 device days. RESULTS The overall infection rate for CA-UTI, IV-CRBSI, and VAP were found to be 0.6, 0.48, and 21.92 per 1000 device days, respectively. The organisms isolated were Staphylococcus aureus, CONS, Enterococci, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. CONCLUSIONS Duration of indwelling devices was found to be the major risk-factor for acquiring DAIs. Low DAI rate might have been due to use of antibiotics, often prophylactic. Active surveillance is quite a tedious and time-consuming process; however the outcome is useful in prevention and control of DAIs.
Intensity Data Correction for the Distance Effect in Terrestrial Laser Scanners

Terrestrial laser scanning systems deliver geographic coordinates and backscattered intensity values, which are acknowledged as significant observations that can be used in a wide range of applications. However, the direct use of these original intensity data is not recommended because they are influenced by multiple variables, especially distance and incidence angle effects. Multiple studies have demonstrated the success of the Lambertian cosine law in correcting the incidence angle effect. The distance effect, which is inconsistent with the theoretical relationships of the laser range equation, is complex and differs significantly across various systems. In this study, the effect of distance on intensity data is investigated. A new correction method for different scanners is proposed. Using diffuse targets at different reflectance values, two sets of experiments are designed to estimate the parameters and validate the proposed method. Faro Focus3D 120 and Faro Focus3D X330 terrestrial scanners are utilized; results show that the ratio of the coefficient of variation of the corrected intensity to that of the original intensity of the said scanners is approximately 0.19 and 0.07, respectively. The proposed method is also applied to correct the distance effect of natural surfaces and to investigate its practicability. The results imply that the proposed method exhibits high accuracy and generality in removing the distance effect and can be used for actual mapping tasks and geological applications.
Neonatal Ovine Uterine Development Involves Alterations in Expression of Receptors for Estrogen, Progesterone, and Prolactin1

Abstract Effects of age on uterine histoarchitecture, cell proliferation, and hormone receptor expression were determined for neonatal ewe lambs from birth (Postnatal Day [PND] 0) to PND 56. Uteri were histologically evaluated and proliferating cell nuclear antigen (PCNA), estrogen receptor alpha (ER-α), progesterone receptor (PR), and prolactin receptor (PRL-R) expression were characterized by in situ hybridization (ISH), immunohistochemistry, or both. The most striking feature of neonatal uterine development was the genesis and development of glands in the intercaruncular areas of endometrium. After birth, endometrial glandular epithelium (GE) budded and differentiated into the underlying stroma from the luminal epithelium (LE) between PNDs 1 and 7. Between PNDs 14 and 56, extensive coiling and branching morphogenesis of nascent endometrial glands occurred. By PND 56, the uterine wall appeared to be histoarchitecturally mature. At birth, nuclear PCNA protein was strongly detected in LE. Between PNDs 7 and 56, high levels of PCNA, ER-α, and PR gene expression were detected in both nascent and developing GE. Higher levels of PCNA and ER-α expression were detected in GE at the tips of developing glands as well as in the surrounding stroma. Progesterone was below detectable limits in serum. Serum estradiol-17β levels were high on PND 1, increased from PNDs 14 to 28, and declined from PND 42 to PND 56. Serum PRL levels increased from PNDs 1 to 14 and declined thereafter. Using ISH and reverse transcriptase-polymerase chain reaction (RT-PCR) analysis, expression of mRNAs for short and long forms of the ovine PRL-R were first detected in nascent GE on PND 7 and increased between PNDs 7 and 56 in proliferating and differentiating GE. These results indicate that 1) uterine gland genesis is initiated between PNDs 1 and 7 after birth and is essentially completed by PND 56; 2) neonatal uterine morphogenesis involves temporal and spatial alterations in cell proliferation and ER-α, PR, and PRL-R gene expression; 3) PRL-R expression is a unique marker of GE differentiation and proliferation; and 4) serum estradiol-17β and PRL levels increase during the onset of GE tubular branching morphogenesis. Results support the hypothesis that neonatal ovine uterine development involves epithelial PRL-R and ER-α activation to stimulate and maintain endometrial gland genesis and branching morphogenesis.
Improved prediction of awakening or nonawakening from severe anoxic coma using tree-based classification analysis*

Objective:To evaluate the utility of sensory and event-related evoked potentials for the prediction of awakening/nonawakening in severe anoxic coma and to design a decision tree helping decision for any patient in this condition. Design:Prospective cohort study. Setting:Clinical neurophysiology unit and intensive care unit of a French university hospital. Patients:Sixty-two consecutive severe comatose patients after out-of-hospital cardiac arrest. Interventions:None Measurements and Main Results:We gathered clinical variables and recorded the somatosensory, auditory, and cognitive evoked potentials within an average period of 8 days after cardiac arrest. The patients were followed for 12 months and classified as awake or nonawake (permanent vegetative state or death). The statistical study included measurements of specificity, sensitivity, and positive and negative predictive value for each clinical and electrophysiologic variable recorded at the early stage of coma. Furthermore, a tree-based classification analysis was performed. All patients in whom somatosensory evoked potentials or middle-latency auditory evoked potentials were abolished did not awaken (100% specificity). All patients in whom mismatch negativity (MMN) was present awakened (100% specificity). MMN was superior to somatosensory evoked potentials for the prediction of awakening and had the best specificity and positive predictive value for awakening. On the decision tree, the awakening/nonawakening explicative variables were, by order of importance, MMN, pupillary reactivity, and somatosensory evoked potentials. Conclusions:There is a need to predict early and accurately awakening or nonawakening in postanoxic comas. Using sensory and cognitive evoked potentials to assess the functional condition of the brain, a prognostic tree for the prediction of awakening/nonawakening in severe anoxic coma has been designed. It is applicable to any patient in this condition and offers the possibility to predict with very high probability awakening when MMN, the earliest component of event-related potentials, is present and nonawakening when MMN and pupillary light reflex are absent or cortical components of somatosensory evoked potentials are abolished.
Process Evaluation of the Enabling Mothers to Prevent Pediatric Obesity Through Web-Based Learning and Reciprocal Determinism (EMPOWER) Randomized Control Trial

Family-and-home-based interventions are an important vehicle for preventing childhood obesity. Systematic process evaluations have not been routinely conducted in assessment of these interventions. The purpose of this study was to plan and conduct a process evaluation of the Enabling Mothers to Prevent Pediatric Obesity Through Web-Based Learning and Reciprocal Determinism (EMPOWER) randomized control trial. The trial was composed of two web-based, mother-centered interventions for prevention of obesity in children between 4 and 6 years of age. Process evaluation used the components of program fidelity, dose delivered, dose received, context, reach, and recruitment. Categorical process evaluation data (program fidelity, dose delivered, dose exposure, and context) were assessed using Program Implementation Index (PII) values. Continuous process evaluation variables (dose satisfaction and recruitment) were assessed using ANOVA tests to evaluate mean differences between groups (experimental and control) and sessions (sessions 1 through 5). Process evaluation results found that both groups (experimental and control) were equivalent, and interventions were administered as planned. Analysis of web-based intervention process objectives requires tailoring of process evaluation models for online delivery. Dissemination of process evaluation results can advance best practices for implementing effective online health promotion programs.
Harmonic feedback-loop oscillator for pulling effect reduction and improved phase noise

A diplexer-based harmonic feedback-loop oscillator concept is presented and demonstrated at 5.8GHz. Without additional complexity, the diplexer together with an RF amplifier creates isolation between nonlinear feedback-loop dynamics and second harmonic signal component that is directed to the output. As a result, the load pulling effect is reduced as well as the phase noise performance is improved with reference to its fundamental feedback-loop counterpart. Load-pull measured results (VSWR ≤ 9) are observed follows: 1) load dependent frequency drift is significantly reduced from -19<sup>0</sup>/<sub>00</sub>~15<sup>0</sup>/<sub>00</sub> to -0.75<sup>0</sup>/<sub>00</sub>~1.06<sup>0</sup>/<sub>00</sub>; 2) phase noise at 1MHz offset is improved by 15dB; and 3) output power is slightly affected only.
Developmental expression of matrix metalloproteinases 2 and 9 and their potential role in the histogenesis of the cerebellar cortex

The development of the cerebellar cortex depends on intrinsic genetic programs and orchestrated cell–cell/cell–matrix interactions. Matrix metalloproteinases (MMPs) are proteolytic enzymes that play an important role in these interactions. MMP‐2 and MMP‐9 are involved in diverse neuronal functions including migration, process extension, and synaptic plasticity. We investigated the spatiotemporal pattern of expression/activity of MMP‐2/MMP‐9 in the developing cerebellum and their role in the histogenesis of the cerebellar cortex. The levels of transcripts of MMP‐2/MMP‐9 were measured with real‐time quantitative polymerase chain reaction. An initial decrease in MMP‐2/MMP‐9 transcripts was observed between postnatal days 3 (PD3) and PD6, and the mRNA levels remained relatively constant thereafter. Zymographic analysis revealed that the expression/activity of MMP‐2/MMP‐9 persisted longer than their transcripts; the downregulation occurred around PD9, suggesting a mechanism of translational or post‐translational regulation. The gelatinase activity was localized in the external granule layer (EGL) and the internal granule layer during PD3–PD12. The immunoreactivity of MMP‐2 was mainly localized in the EGL, the Bergmann glial fibers, and the Purkinje cell layer (PCL), whereas MMP‐9 immunoreactivity was detected intensively in the PCL and the extracellular space of the molecular layer. Expression of MMP‐9 was relatively weak in the EGL. The immunoreactivity of MMP‐2/MMP‐9 became undetectable after PD21. A similar expression pattern of MMP‐2/MMP‐9 was observed in organotypic cerebellar slice cultures. Exposure of organotypic slices to a specific MMP‐2/MMP‐9 inhibitor significantly increased the thickness of the EGL and concurrently decreased the number of migrating granule neurons in the molecular layer. Thus, MMP‐2 and MMP‐9 play a role in the postnatal cerebellar morphogenesis. J. Comp. Neurol. 481:403–415, 2005. © 2004 Wiley‐Liss, Inc.
Skewing of the brain midline in schizophrenia

Our laboratory has observed marked craniofacial dysmorphology along the frontonasal-maxillary juncture in schizophrenic probands and their relatives. Embryologic fate-mapping studies relate this craniofacial juncture to the diencephalic-mesencephalic border, and on the basis of this correspondence we have predicted brain midline maldevelopment arising at this border in schizophrenia. Analysis of magnetic resonance images has borne out this prediction, with midline deviation scores in schizophrenia exceeding control values. High deviation scores were also observed among the siblings of these schizophrenic patients. Further, brain and face dysmorphology scores cohered within subjects, supporting this embryologically derived model.
Appreciative Inquiry for Quality Improvement in Primary Care Practices

Purpose: To test the effect of an Appreciative Inquiry (AI) quality improvement strategy on clinical quality management and practice development outcomes. Appreciative inquiry enables the discovery of shared motivations, envisioning a transformed future, and learning around the implementation of a change process. Methods: Thirty diverse primary care practices were randomly assigned to receive an AI-based intervention focused on a practice-chosen topic and on improving preventive service delivery (PSD) rates. Medical-record review assessed change in PSD rates. Ethnographic field notes and observational checklist analysis used editing and immersion/crystallization methods to identify factors affecting intervention implementation and practice development outcomes. Results: The PSD rates did not change. Field note analysis suggested that the intervention elicited core motivations, facilitated development of a shared vision, defined change objectives, and fostered respectful interactions. Practices most likely to implement the intervention or develop new practice capacities exhibited 1 or more of the following: support from key leader(s), a sense of urgency for change, a mission focused on serving patients, health care system and practice flexibility, and a history of constructive practice change. Conclusions: An AI approach and enabling practice conditions can lead to intervention implementation and practice development by connecting individual and practice strengths and motivations to the change objective.
Mini-incision Patellar Tendon Harvest and Anterior Cruciate Ligament Reconstruction Using Critical Bony Landmarks

Graft choice remains an area of contention in anterior cruciate ligament reconstruction. Poorer cosmetic results and anterior knee pain remain a problem in the use of autologous patellar tendon grafts despite excellent clinical results when compared with autologous hamstring tendon grafts. Using a 2-incision technique to harvest the patellar tendon grafts has been shown to decrease the risk of anterior knee pain to a level comparable to hamstring tendon grafts. Proper graft tunnel placement and orientation also remain controversial with several recent researchers arguing the ability to perform an anatomic reconstruction using a conventional endoscopic transtibial technique. We will describe a relatively simple and cosmetically acceptable 2-incision technique for harvesting a bone-tendon-bone graft. In addition, we will describe the bony landmarks that should be used to ensure proper anatomic graft placement and the appropriate angles that need to be used for the tibial tunnel to drill the femoral tunnel in an anatomic position and carry out a successful endoscopic transtibial tunnel anterior cruciate ligament reconstruction.
Human ADP-ribosylation Factor-activated Phosphatidylcholine-specific Phospholipase D Defines a New and Highly Conserved Gene Family (*)

Activation of phosphatidylcholine-specific phospholipase D (PLD) has been implicated as a critical step in numerous cellular pathways, including signal transduction, membrane trafficking, and the regulation of mitosis. We report here the identification of the first human PLD cDNA, which defines a new and highly conserved gene family. Characterization of recombinant human PLD1 reveals that it is membrane-associated, selective for phosphatidylcholine, stimulated by phosphatidylinositol 4,5-bisphosphate, activated by the monomeric G-protein ADP-ribosylation factor-1, and inhibited by oleate. PLD1 likely encodes the gene product responsible for the most widely studied endogenous PLD activity.
Automatic band detection of 1D-gel images

Many gel electrophoresis image segmentation methods have been proposed. However, most of the proposed methods cannot provide a satisfying performance since a gel electrophoresis image is a manually captured image often with various noise and poor quality. This paper presents a 1D-gel image segmentation method (1DGISM) to cut the bands from a one-dimension gel electrophoresis image (1D-gel image). The experimental results showed that 1DGISM can give an impressive segmentation performance even if the band boundaries are indistinct.