Miracle-dz/UniFAR-FTUs huggingface dataset:
THE SUSCEPTIBILITY OF MICE TO BACTERIAL ENDOTOXINS

Albino mice (Rockefeller NCS strain) raised and maintained free of ordinary bacterial pathogens, as well as of intestinal Escherichia coli and of Proteus bacilli, were found to be highly resistant to the lethal effect of bacterial endotoxins. When newborn mice of this NCS colony were nursed by foster mothers from another colony raised under ordinary conditions (SS colony from which the NCS colony was derived), they acquired the intestinal flora of the latter animals and became susceptible to the lethal effects of endotoxins. NCS adult mice could be rendered susceptible to the lethal effect of endotoxins by vaccination with heat killed Gram-negative bacilli. The susceptibility thus induced exhibited a certain degree of specificity for the bacterial strain used in vaccination. Although untreated NCS mice were resistant to the lethal effect of endotoxins, they proved exquisitively susceptible to the infection-enhancing effect of these materials. For example, 1 µg. or less of endotoxin was found sufficient to help establish a rapidly fatal septicemia with Staphylococcus aureus. Small amounts of endotoxin (1 µg. or less), administered alone, caused a marked but transient loss of weight. Vaccination with heat-killed Gram-negative bacilli or with killed BCG increased the resistance of NCS mice to the infection-enhancing effect of small amounts of endotoxin. This protective effect exhibited a certain degree of specificity for the bacterial strain from which the toxin used in the infection-enhancing test was derived. These various findings can be explained by assuming that the pathological effects of endotoxins involve at least two unrelated mechanisms; (a) a primary toxicity illustrated in this study by the loss of weight and enhancement of infection resulting from the injection of small doses of toxin; (b) an immunological reaction with lethal consequences which became manifest only in animals sensitized to the endotoxin by prior exposure to Gram-negative bacilli.
When vision is not an option: children’s integration of auditory and haptic information is suboptimal

When visual information is available, human adults, but not children, have been shown to reduce sensory uncertainty by taking a weighted average of sensory cues. In the absence of reliable visual information (e.g. extremely dark environment, visual disorders), the use of other information is vital. Here we ask how humans combine haptic and auditory information from childhood. In the first experiment, adults and children aged 5 to 11 years judged the relative sizes of two objects in auditory, haptic, and non-conflicting bimodal conditions. In Experiment 2, different groups of adults and children were tested in non-conflicting and conflicting bimodal conditions. In Experiment 1, adults reduced sensory uncertainty by integrating the cues optimally, while children did not. In Experiment 2, adults and children used similar weighting strategies to solve audio–haptic conflict. These results suggest that, in the absence of visual information, optimal integration of cues for discrimination of object size develops late in childhood.
Class 3 Semaphorin Mediates Dendrite Growth in Adult Newborn Neurons through Cdk5/FAK Pathway

Class 3 semaphorins are well-known axonal guidance cues during the embryonic development of mammalian nervous system. However, their activity on postnatally differentiated neurons in neurogenic regions of adult brains has not been characterized. We found that silencing of semaphorin receptors neuropilins (NRP) 1 or 2 in neural progenitors at the adult mouse dentate gyrus resulted in newly differentiated neurons with shorter dendrites and simpler branching in vivo. Tyrosine phosphorylation (Tyr 397) and serine phosphorylation (Ser 732) of FAK were essential for these effects. Semaphorin 3A and 3F mediate serine phosphorylation of FAK through the activation of Cdk5. Silencing of either Cdk5 or FAK in newborn neurons phenocopied the defects in dendritic development seen upon silencing of NRP1 or NRP2. Furthermore, in vivo overexpression of Cdk5 or FAK rescued the dendritic phenotypes seen in NRP1 and NRP2 deficient neurons. These results point to a novel role for class 3 semaphorins in promoting dendritic growth and branching during adult hippocampal neurogenesis through the activation of Cdk5-FAK signaling pathway.
Light Inhibits COP1-Mediated Degradation of ICE Transcription Factors to Induce Stomatal Development in Arabidopsis

Light inhibits the COP1-directed degradation of ICE transcription factors, which act as activators of stomatal development in Arabidopsis. Stomata are epidermal openings that facilitate plant-atmosphere gas exchange during photosynthesis, respiration, and water evaporation. Stomatal differentiation and patterning are spatially and temporally regulated by the master regulators SPEECHLESS (SPCH), MUTE, and FAMA, which constitute a central gene regulatory network along with Inducer of CBF Expression (ICE) transcription factors for this developmental process. Stomatal development is also profoundly influenced by environmental conditions, such as light, temperature, and humidity. Light induces stomatal development, and various photoreceptors modulate this response. However, it is unknown how light is functionally linked with the master regulatory network. Here, we demonstrate that, under dark conditions, the E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) degrades ICE proteins through ubiquitination pathways in leaf abaxial epidermal cells in Arabidopsis thaliana. Accordingly, the ICE proteins accumulate in the nuclei of leaf abaxial epidermal cells in COP1-defective mutants, which constitutively produce stomata. Notably, light in the blue, red, and far-red wavelength ranges suppresses the COP1-mediated degradation of the ICE proteins to induce stomatal development. These observations indicate that light is directly linked with the ICE-directed signaling module, via the COP1-mediated protein surveillance system, in the modulation of stomatal development.
Increasing the Participation of Under-represented Minority Student Groups in Computer Science and Engineering: An REU Site Experience

Statistics indicate that under-represented minority student groups continue to experience high dropout rates, low graduation rates, low enrollment in graduate programs and low participation in computer science and engineering (CS&E). At the same time, trends indicate that these groups will constitute an important part of the population of the United States by year 2050. Given these facts, it is crucial to help these minority groups become an integral part of the economic fabric of the United States. It has been shown that undergraduate research is one of the best vehicles to address several of these important issues. This paper describes our experience running a NSF-sponsored research experiences for undergraduates (REU) site in CS&E for under-represented minority student groups. We describe the most important aspects that need to be included in these programs and some strategies for running them successfully. Finally, we include the results of our evaluation and show the effectiveness of the program
Terminology and Reporting Criteria for Radiofrequency Ablation of Tumors in the Scientific Literature: Systematic Review of Compliance with Reporting Standards

Objective To perform a systematic review of compliance with standardized terminology and reporting criteria for radiofrequency (RF) tumor ablation, proposed by the International Working Group on Image-Guided Tumor Ablation in 2003, in the published reports. Materials and Methods Literature search in the PubMed database was performed using index keywords, PubMed limit system, and eligibility criteria. The entire content of each article was reviewed to assess the terminology used for procedure terms, imaging findings, therapeutic efficacy, follow-up, and complications. Accuracy of the terminology and the use of alternative terms instead of standard terminology were analyzed. In addition, disparities in accuracy of terminology in articles according to the medical specialty and the type of radiology journal were evaluated. Results Among the articles (n = 308) included in this study, the accuracy of the terms 'procedure or session', 'treatment', 'index tumor', 'ablation zone', 'technical success', 'primary technique effectiveness rate', 'secondary technique effectiveness rate', 'local tumor progression', 'major complication', and 'minor complication' was 97% (298/307), 97% (291/300), 8% (25/307), 65% (103/159), 55% (52/94), 33% (42/129), 94% (17/18), 45% (88/195), 99% (79/80), and 100% (77/77), respectively. The overall accuracy of each term showed a tendency to improve over the years. The most commonly used alternative terms for 'technical success' and 'local tumor progression' were 'complete ablation' and 'local (tumor) recurrence', respectively. The accuracy of terminology in articles published in radiology journals was significantly greater than that of terminology in articles published in non-radiology journals, especially in Radiology and The Journal of Vascular and Interventional Radiology. Conclusion The proposal for standardization of terminology and reporting criteria for RF tumor ablation has been gaining support according to the recently published scientific reports, especially in the field of radiology. However, more work is still needed for the complete standardization of terminology.
Preventable Major Cardiovascular Events Associated With Uncontrolled Glucose, Blood Pressure, and Lipids and Active Smoking in Adults With Diabetes With and Without Cardiovascular Disease: A Contemporary Analysis

OBJECTIVE The objective of this study was to assess the incidence of major cardiovascular (CV) hospitalization events and all-cause deaths among adults with diabetes with or without CV disease (CVD) associated with inadequately controlled glycated hemoglobin (A1C), high LDL cholesterol (LDL-C), high blood pressure (BP), and current smoking. RESEARCH DESIGN AND METHODS Study subjects included 859,617 adults with diabetes enrolled for more than 6 months during 2005–2011 in a network of 11 U.S. integrated health care organizations. Inadequate risk factor control was classified as LDL-C ≥100 mg/dL, A1C ≥7% (53 mmol/mol), BP ≥140/90 mm Hg, or smoking. Major CV events were based on primary hospital discharge diagnoses for myocardial infarction (MI) and acute coronary syndrome (ACS), stroke, or heart failure (HF). Five-year incidence rates, rate ratios, and average attributable fractions were estimated using multivariable Poisson regression models. RESULTS Mean (SD) age at baseline was 59 (14) years; 48% of subjects were female, 45% were white, and 31% had CVD. Mean follow-up was 59 months. Event rates per 100 person-years for adults with diabetes and CVD versus those without CVD were 6.0 vs. 1.7 for MI/ACS, 5.3 vs. 1.5 for stroke, 8.4 vs. 1.2 for HF, 18.1 vs. 40 for all CV events, and 23.5 vs. 5.0 for all-cause mortality. The percentages of CV events and deaths associated with inadequate risk factor control were 11% and 3%, respectively, for those with CVD and 34% and 7%, respectively, for those without CVD. CONCLUSIONS Additional attention to traditional CV risk factors could yield further substantive reductions in CV events and mortality in adults with diabetes.
Sensing and Integration of Erk and PI3K Signals by Myc

The transcription factor Myc plays a central role in regulating cell-fate decisions, including proliferation, growth, and apoptosis. To maintain a normal cell physiology, it is critical that the control of Myc dynamics is precisely orchestrated. Recent studies suggest that such control of Myc can be achieved at the post-translational level via protein stability modulation. Myc is regulated by two Ras effector pathways: the extracellular signal-regulated kinase (Erk) and phosphatidylinositol 3-kinase (PI3K) pathways. To gain quantitative insight into Myc dynamics, we have developed a mathematical model to analyze post-translational regulation of Myc via sequential phosphorylation by Erk and PI3K. Our results suggest that Myc integrates Erk and PI3K signals to result in various cellular responses by differential stability control of Myc protein isoforms. Such signal integration confers a flexible dynamic range for the system output, governed by stability change. In addition, signal integration may require saturation of the input signals, leading to sensitive signal integration to the temporal features of the input signals, insensitive response to their amplitudes, and resistance to input fluctuations. We further propose that these characteristics of the protein stability control module in Myc may be commonly utilized in various cell types and classes of proteins.
Molecular Modeling of Chem-Bio (CB) Contaminant Sorption/Desorption and Reactions in Chlorinated Water Systems

Abstract : Army installations contain a high density of mission-critical buildings that require constant protection from accidental or deliberate contamination of water distribution systems. Current simulations of contaminant fate and transport in pipe systems do not accurately portray reality. The simulations assume pure hydraulic transport of contaminants and do not account for sorption of the contaminant on pipe walls. Additionally, subsequent reactions such as hydrolysis are not considered. These omissions reduce predictability of a contaminant s progression and effect in the distribution system. In addition, inadequate understanding of contaminant fate and transport may result in an unacceptable risk to mission readiness. However, performing laboratory tests for every known and emerging chemical or biological contaminant to obtain uptake and reaction parameters is not feasible with regard to time or cost investments. This report documents advances in molecular modeling predictions for the transport of contaminants using: the Nanoscale Molecular Dynamics program, the influence of bacterial biofilms on spore viability within a chlorinated water distribution system, the computational chemistry predictions of the rate of hydrolysis of a specific contaminant, and the inclusion of results into the pre-dictive software, EPANet. This work opens the way for better vulnerability assessments, protection, real-time response, remediation, and planning.
Nonbinary Cyclic LDPC Codes Derived from Idempotents and Modular Golomb Rulers

Based jointly on idempotents and modular Golomb rulers, we construct a class of nonbinary cyclic low-density parity-check (LDPC) codes. The defining parity-check matrix is a sparse circulant, on which we put two constraints: 1) the characteristic polynomial is an idempotent, 2) the nonzero elements of the first row are located on a modular Golomb ruler. We show that the second constraint forms a necessary and sufficient condition for the Tanner graph to have no cycles of length 4. The minimum distance of the code is proved equal to the column weight of the parity-check matrix plus one. A search algorithm is presented, with which we obtain some high rate codes with large minimum distances. The issue of code equivalence is also discussed. Simulation results show that the obtained codes perform well under iterative decoding.
The dual tree of a recursive triangulation of the disk

In the recursive lamination of the disk, one tries to add chords one after another at random; a chord is kept and inserted if it does not intersect any of the previously inserted ones. Curien and Le Gall [Ann. Probab. 39 (2011) 2224-2270] have proved that the set of chords converges to a limit triangulation of the disk encoded by a continuous process $\mathscr{M}$. Based on a new approach resembling ideas from the so-called contraction method in function spaces, we prove that, when properly rescaled, the planar dual of the discrete lamination converges almost surely in the Gromov-Hausdorff sense to a limit real tree $\mathscr{T}$, which is encoded by $\mathscr{M}$. This confirms a conjecture of Curien and Le Gall.
Synthesis of Framework Isomer MOFs Containing Zinc and 4-Tetrazolyl Benzenecarboxylic Acid via a Structure Directing Solvothermal Approach

The solvothermal synthesis of framework isomers was carried out using the hybrid carboxylate and tetrazolate functional ligand, 4-tetrazolyl benzenecarboxylic acid (H2TBC, TBC = 4-tetrazolyl benzenecarboxylate) and zinc. H2TBC was also synthesized with the solvothermal approach, and is referred herein as structure 1. Using single-crystal X-ray diffraction, we found that the tetrazolate groups of TBC show an unusual “opposite-on” coordination mode with zinc. Three previously characterized metal-organic frameworks (MOFs) were obtained by systematically changing the solvents of the H2TBC-Zn reaction, (1) ZnTBC, 2, which has a non-porous structure; (2) Zn2(TBC)2(H2O), 3, which has an amphiphilic pore structure and (3) Zn2(TBC)2{guest}, 4, which is porous and has channels containing uncoordinated N heteroatoms. Fluorescence spectra of 4 reveal a strong blue emission mainly from the TBC ligands.
Experimental Investigation of In-Plane Constraint and Out-of-Plane Constraint Effects on Creep Crack Growth

In order to establish an accurate integrity assessment of structures containing defects at high temperature, it is necessary to clarify the constraint effect on creep crack growth (CCG) property. However, the experimental investigation of constraint effects on creep crack growth has been little studied. In this study, the effects of the out-of-plane constraint and the in-plane constraint were investigated and considered via data obtained from compact tension (CT) specimens with different thicknesses and single edge-notched tensile (SENT) specimen. The results show that the constraint effect induced by specimen thickness (out-of-plane) and specimen types (in-plane) on CCG rate is related to load level C*. In the lower C* region, there are obvious differences in the CCG rate for different specimens, while the CCG rates of the different specimens are within a scatter band in the higher C* region. Meanwhile, the CCG rate da/dt versus C* on log-log scale is composed of two straight lines with different slops instead of a single linear relation. Because the straight line slope in the lower C* region is smaller than that in the higher C* region, it would be non-conservative if the CCG rate in the lower C* was extrapolated from that in the higher C*. Therefore, in order to conduct integrity assessment and life prediction at high temperature accurately, it is necessary to obtain the actual CCG rate in the lower C* (long-term data), and the constraint effect induced by specimen thickness and loading modes should be considered.Copyright © 2012 by ASME
Infrequent detection of cytomegalovirus and Epstein-Barr virus DNA in synovial membrane of patients with rheumatoid arthritis.

OBJECTIVE To study the role of the cytomegalovirus (CMV), Epstein-Barr virus (EBV), herpes simplex virus types 1 and 2 (HSV-1 and 2), varicella zoster virus (VZV), and human herpes virus 6 (HHV-6) in the etiology of rheumatoid arthritis (RA). METHODS Polymerase chain reaction (PCR) was used to detect DNA of the different herpes viruses in synovial membranes from 31 patients with chronic RA and 14 control patients. Specific antibodies were determined by indirect immunofluorescence and ELISA. RESULTS Out of 31 patients with RA, CMV DNA was detected in synovial membranes from 2 patients and EBV DNA was detected in synovial membranes from 2 other patients. All samples from the patients with RA were negative for DNA from HSV-1 and 2, VZV, and HHV-6. All samples from the 14 control patients were negative in all PCR assays. No statistically significant differences in IgG antibodies were found for CMV, HSV-1, VZV, and HHV-6 in patients with RA compared to controls. Higher titers of IgG antibodies against EBV viral capsid antigen were found in patients with RA, with a significance of p < 0.05. CONCLUSION Both CMV and EBV DNA were detected in synovial membranes from 6% of the patients with RA. We cannot exclude the possibility that these viruses were associated with disease development in a minority of patients with RA.
Frequency of anti-Chlamydia trachomatis antibodies in infertile women referred to Tabriz Al-Zahra hospital

Background: Infertility is one of the major issues in society and its incidence is estimated to be almost 10-15%. Chlamydia trachomatis (C. trachomatis) is an important cause of sexually transmitted diseases leading to infertility. Objective: This study was designed to determine the frequency of anti-C. trachomatis antibodies in infertile women at Al-zahra hospital, Tabriz, Iran. Materials and Methods: In this cross-sectional study, the blood samples were collected randomly from 184 infertile women (case group) and 100 pregnant women (control group). The frequency of specific IgG and IgM anti-C. trachomatis antibodies were evaluated using ELISA method. Results: The frequency of IgG anti-C. trachomatis antibody in the control and case groups was 18% and 35.88%, respectively. IgM anti-C. trachomatis antibody was found in 2% of controls and 5.44% of infertile women. Our results showed the significant differences between the case and control groups in anti-C. trachomatis antibodies (IgG, p=0.035 and IgM, p=0.004). Also, no significant relation was seen between the frequency of anti-C. trachomatis antibodies and age, location, and tubal factor infertility in our two study groups. Conclusion: According to high frequency of antibody anti-C. trachomatis among infertile women in competition to the control group, evaluation and treatment of Chlamydia infections is necessary in these patients.
Falling into the coverage gap: Part D drug costs and adherence for Medicare Advantage prescription drug plan beneficiaries with diabetes.

OBJECTIVE To compare drug costs and adherence among Medicare beneficiaries with the standard Part D coverage gap versus supplemental gap coverage in 2006. DATA SOURCES Pharmacy data from Medicare Advantage Prescription Drug (MAPD) plans. STUDY DESIGN Parallel analyses comparing beneficiaries aged 65+ with diabetes in an integrated MAPD with a gap versus no gap (n=28,780); and in a network-model MAPD with a gap versus generic-only coverage during the gap (n=14,984). PRINCIPAL FINDINGS Drug spending was 3 percent (95 percent confidence interval [CI]: 1-4 percent) and 4 percent (CI: 1-6 percent) lower among beneficiaries with a gap versus full or generic-only gap coverage, respectively. Out-of-pocket expenditures were 189 percent higher (CI: 185-193 percent) and adherence to three chronic drug classes was lower among those with a gap versus no gap (e.g., odds ratio=0.83, CI: 0.79-0.88, for oral diabetes drugs). Annual out-of-pocket spending was 14 percent higher (CI: 10-17 percent) for beneficiaries with a gap versus generic-only gap coverage, but levels of adherence were similar. CONCLUSIONS Among Medicare beneficiaries with diabetes, having the Part D coverage gap resulted in lower total drug costs, but higher out-of-pocket spending and worse adherence compared with having no gap. Having generic-only coverage during the gap appeared to confer limited benefits compared with having no gap coverage.