Miracle-dz/UniFAR-FTUs huggingface dataset:
Disseminated Gonococcal Infection: A Prospective Analysis of 49 Patients and a Review of Pathophysiology and Immune Mechanisms

Forty-nine patients with disseminated gonococcal infection (DGI) hospitalized at Boston City and University Hospitals over a 7-year period were studied. Patients with clinical manifestations of DGI and with cervical, urethral, rectal, pharyngeal, synovial or blood cultures positive for Neisseria gonorrhoeae were separated into two groups based on the presence or absence of suppurative arthritis. There were 19 cases of suppurative arthritis (Group II) and 30 cases with only tenosynovitis, skin lesions, or both (Group I). Blood cultures were positive only in Group I patients (43%) and synovial fluid cultures only in Group II patients (47%). Polyarthralgia was the most common initial symptom in both groups of patients. Twenty-six Group I patients had tenosynovitis (87%), while only 4 Group II patients (21%) had tenosynovitis (p less than 0.001). The knee was the most commonly involved suppurated joint. Twenty-seven Group I patients (90%) had skin lesions compared to 8 Group II patients (42%) (p less than 0.001). Some of these lesions progressed on treatment; some patients were unaware of their lesions. Genitourinary symptoms were unusual in both groups of patients. Eleven women (33%) were menstruating or were pregnant at the onset of DGI. Thirteen patients had histories suggestive of previous gonococcal infections; one had recurrent DGI. This patient and one other were found to have complement abnormalities. There were no cases of endocarditis or meningitis. Four patients had unexplained liver function abnormalities. All patients recovered uneventfully. Strains isolated from disseminated sites were predominantly of the transparent phenotype (90%). Many strains (58%) required arginine, hypoxanthine and uracil for growth. They were also more susceptible to penicillin than reported strains that cause pelvic inflammatory disease. Most strains were of a single outer membrane protein coagglutination serogroup, WI (85%). These characteristics did not vary between the Group I and Group II isolates. The two groups of strains, however, did vary in their complement-dependent bactericidal reactivity to normal human sera. Eighteen of 24 Group I strains (75%) versus 9 of 19 Group II strains (47%) resisted killing by all normal human sera tested (p less than .05). Likewise, convalescent sera from Group II patients were able to kill their infecting strains more often than did sera from Group I patients (70% vs 17%) (p less than 0.01). Thus, variations in the clinical expression of disease in patients with DGI may be explained, in part, by differences in certain phenotypic and immunologic features of infecting strains.
Human Capital Accumulation of Disabled Children:Does Disability Really Matter?

Si la majoritA© de la population handicapA©e dans le monde vit dans les pays en voie de dA©veloppement, on ne sait pourtant que trA¨s peu de choses sur les consA©quences du handicap dans ces rA©gions du monde. Ce travail utilise les donnA©es de lâ€™EnquAate DA©mographique et de SantA© A Indicateurs Multiples (DHS-MICS) 2011 afin dâ€™A©valuer lâ€™effet du handicap des enfants sur lâ€™A©ducation de ces derniers au Cameroun. Cet effet est A©galement A©valuA© A la fois sur la frA©quentation scolaire et sur la rA©ussite scolaire et suivant la sA©vA©ritA© du handicap. Lâ€™apport scientifique de ce travail rA©side dans le fait que, dans un contexte dâ€™abscence de donnA©es longitudinales, les estimations des effets du handicap sont corrigA©es A la fois du biais dâ€™endogA©nA©itA© liA© aux inobservables A travers un modA¨le A effets-fixes famille et A effets-fixes fratrie, et du biais liA© A la simultanA©itA© grA¢ce A lâ€™utilisation du handicap de naissance. Il en rA©sulte que le handicap modA©rA© et le handicap sA©vA¨re de lâ€™enfant rA©duisent de 9% et 42% sa probabilitA© de frA©quenter actuellement lâ€™A©cole et de 8% et 55% respectivement sa probabilitA© dâ€™avoir dA©jA A©tA© lâ€™A©cole. Le handicap, lorsquâ€™il est modA©rA©, mais plus encore lorsquâ€™il est sA©vA¨re, rA©duit la rA©ussite scolaire, montrant que le faible niveau dâ€™A©ducation des enfants handicapA©s nâ€™est pas unique dA» au problA¨me dâ€™accA¨s A lâ€™A©cole.
Propagation of target and organ at risk contours in radiotherapy of prostate cancer using deformable image registration

Abstract Background. Successful deformable image registration is an essential component of both dose accumulation and plan adaptation in radiotherapy. The aim of this study was to evaluate the performance of a deformable image registration application for propagation of contours using repeat CT scans of the pelvis, a region where considerable deformations are expected. Material and methods. The study involved four prostate cancer patients, each with 9–11 repeat CT scans. An oncologist contoured bladder, rectum, clinical target volume of pelvic lymph nodes (CTV-ln) and prostate (CTV-p) in all CT scans. The reference CT was retrospectively registered to the repeat CT scans with both rigid and deformable registration using a recently released commercial clinical software application. Two different diffusion-based ‘demons’ deformable registration algorithms were applied, differing in the amount of deformations being allowed, with algorithm A being more generous than algorithm B. The evaluation of the propagated structures included both quantitative measures and qualitative scoring. Results. We found the differences between the algorithms to be most evident for bladder and rectum. An increase in mean Dice similarity coefficient relative the rigid registrations of 12% and 13% was obtained with algorithm A for bladder and rectum, compared to 2% with algorithm B. For bladder the mean sensitivity and positive predictive value was 0.92 and 0.87 with algorithm A and 0.82 and 0.83 with algorithm B. Corresponding values for rectum was 0.81 and 0.76 with algorithm A and 0.75 and 0.69 with algorithm B. This translated into 57% and 26% passing the clinical evaluation for bladder and rectum, with algorithm A, compared to 17% and 14% with algorithm B. For CTV-ln and CTV-p both algorithms performed well by all measures, e.g. with 86% of the target structures passing the clinical evaluation. Conclusions. Deformable image registration improved contour propagation in the pelvis for all organs investigated. Differences in the performance of the algorithms were seen which became more pronounced for the highly deformable organs of bladder and rectum.
Demographic Stability Metrics for Conservation Prioritization of Isolated Populations

Abstract: Systems of geographically isolated habitat patches house species that occur naturally as small, disjunct populations. Many of these species are of conservation concern, particularly under the interacting influences of isolation and rapid global change. One potential conservation strategy is to prioritize the populations most likely to persist through change and act as sources for future recolonization of less stable localities. We propose an approach to classify long‐term population stability (and, presumably, future persistence potential) with composite demographic metrics derived from standard population‐genetic data. Stability metrics can be related to simple habitat measures for a straightforward method of classifying localities to inform conservation management. We tested these ideas in a system of isolated desert headwater streams with mitochondrial sequence data from 16 populations of a flightless aquatic insect. Populations exhibited a wide range of stability scores, which were significantly predicted by dry‐season aquatic habitat size. This preliminary test suggests strong potential for our proposed method of classifying isolated populations according to persistence potential. The approach is complementary to existing methods for prioritizing local habitats according to diversity patterns and should be tested further in other systems and with additional loci to inform composite demographic stability scores.
Muscarinic Toxin-Like Proteins from Taiwan Banded Krait (Bungarus multicinctus) Venom: Purification, Characterization and Gene Organization

Abstract Two novel proteins, BM8 and BM14, were isolated from Bungarus multicinctus (Taiwan banded krait) venom using the combination of chromatography on a SPSephadex C-25 column and a reversephase HPLC column. Both proteins contained 82 amino acid residues including 10 cysteine residues, but there were two amino acid substitutions at positions 37 and 38 (Glu37Ala38 in BM8; Lys37Lys38 in BM14). CD spectra and acrylamide quenching studies revealed that the gross conformation of BM8 and BM14 differed. In contrast to BM8, BM14 inhibited the binding of [3H]quinuclidinyl benzilate to the M2 muscarinic acetylcholine (mAchR) receptor subtype. Trinitrophenylation of Lys residues abolished the mAchRbinding activity of BM14, indicating that the Lys substitutions at positions 37 and 38 played a crucial role in the activity of BM14. The genomic DNA encoding the precursor of BM14 was amplified by PCR. The gene shared virtually identical structural organization with αneurotoxin and cardiotoxin genes. The intron sequences of these genes shared a sequence identity up to 84%, but the proteincoding regions were highly variable. These results suggest that BM8, BM14, neurotoxins and cardiotoxins may have originated from a common ancestor, and the evolution of snake venom proteins shows a tendency to diversify their functions.
Aluminum nitride as a masking material for the plasma etching of silicon carbide structures

In this paper is detailed a technique for the plasma etching of silicon carbide (SiC) utilizing aluminum nitride (AlN) as a masking material. The fabrication technique enables the use of non-metallic etch masks to etch SiC which can aid in preventing micromasking defects on the etch surface and degradation in the health of plasma etch tools. This is the first report of this fabrication process. Through the experimental characterization of a high density inductively coupled plasma etch tool operated with SF6/O2 chemistries, an etch recipe that yields a SiC etch rate of 0.4 µm/min, a selectivity of 16∶1 (SiC/AlN), and features with a sidewall angle of approximately 10° was developed. In addition, scanning electron microscopy images revealed that the etch recipe yields smooth etch surfaces that are free of micromasking defects. Further investigations of these preliminary results could lead to advancements in the manufacturability of SiC for the development of harsh environment sensing technology and high-power electronics.
Attenuation of Transient Focal Cerebral Ischemic Injury in Transgenic Mice Expressing a Mutant ICE Inhibitory Protein

We used transgenic mice expressing a dominant negative mutation of interleukin-1β converting enzyme (ICE) (C285G) in a model of transient focal ischemia in order to investigate the role of ICE in ischemic brain damage. Transgenic mutant ICE mice (n = 11) and wild-type littermates (n = 9) were subjected to 3 h of middle cerebral artery occlusion followed by 24 h of reperfusion. Cerebral infarcts and brain swelling were reduced by 44% and 46%, respectively. Neurological deficits were also significantly reduced. Regional CBF, blood pressure, core temperature, and heart rate did not differ between groups when measured for up to 1 h after reperfusion. Increases in immunoreactive IL-1β levels, observed in ischemic wild-type brain at 30 min after reperfusion, were 77% lower in the mutant strain, indicating that proIL-1β cleavage is inhibited in the mutants. DNA fragmentation was reduced in the mutants 6 and 24 h after reperfusion. Hence, endogenous expression of an ICE inhibitor confers resistance to cerebral ischemia and brain swelling. Our results indicate that down-regulation of ICE expression might provide a useful therapeutic target in cerebral ischemia.
CD4(+) regulatory T cells in a cynomolgus macaque model of Mycobacterium tuberculosis infection.

BACKGROUND Mycobacterium tuberculosis infection in humans results in either latent infection or active tuberculosis. We sought to determine whether a higher frequency of regulatory T (T(reg)) cells predispose an individual toward active disease or whether T(reg) cells develop in response to active disease. METHODS In cynomolgus macaques infected with a low dose of M. tuberculosis, approximately 50% develop primary tuberculosis, and approximately 50% become latently infected. Forty-one animals were monitored for 6-8 months to assess the correlation of the frequency of Foxp3(+) cells in peripheral blood and airways with the outcome of infection. RESULTS In all animals, the frequency of T(reg) cells (CD4(+)Foxp3(+)) in peripheral blood rapidly decreased and simultaneously increased in the airways. Latently infected monkeys had a significantly higher frequency of T(reg) cells in peripheral blood before infection and during early infection, compared with monkeys that developed active disease. Monkeys with active disease experienced increased frequencies of T(reg) cells among peripheral blood mononuclear cells as they developed disease. CONCLUSIONS Our data suggest that increased frequencies of T(reg) cells in active disease occur in response to increased inflammation rather than act as a causative factor in progression to active disease.
Design and simulation of a solar powered DC home with grid and battery back-up

In an attempt to provide a humble 100W electricity for a DC powered home in an incessant manner, this work deals with the design and implementation of a solar PV based home with uninterrupted power supply. The back-up power is supplied by the power grid and battery. In order to keep output voltage constant, the solar PV is cascaded with a buck converter which has a PWM modulator circuit in its feedback. A Proportional controller adjusts the Kp value which maintains the output voltage at a constant level by appropriately varying the duty ratio of the buck converter. The output of this buck converter is connected to a common DC bus. When solar DC power is unavailable, a reduced voltage 1Φ AC power grid (of 90V) supplies the home through a rectifier and a buck converter which maintains a constant 13.6V DC output. Battery also supplies power in cases when the other two sources are unavailable. Battery is charged either from solar PV or from the rectified AC. A microcontroller design ensures that this 100W DC home is supplied power for maximum amount of time at the minimum possible cost. The proposed scheme has been modeled and simulated in the MATLAB/SIMULINK environment. The test results show that the proposed design exhibits an excellent performance.
Recruitment, screening and characteristics of injection drug users participating in the AIDSVAX®B/E HIV vaccine trial, Bangkok, Thailand

Objectives: To describe recruitment, screening and baseline characteristics of injection drug users (IDU) participating in a phase III HIV vaccine (AIDSVAX®B/E; VaxGen, USA) trial and to compare enrollment characteristics between trial participants and 1209 IDU from a 1995–1998 vaccine trial preparatory cohort for changes that might impact trial design assumptions. Methods: Enrollment for both studies was conducted at Bangkok narcotic treatment clinics, where a standardized questionnaire was administered on demographics, risk behavior and incarceration history over the previous 6 months. Results: During 1999–2000, 4943 IDU were screened for enrollment; successful sources of recruitment included clinic attendees (43.4%), an IDU referral program (20.4%) and preparatory cohort participants (14.7%). Of those screened, 1689 (34%) were HIV seropositive (HIV subtype B 23.6%; subtype E 76.4%). Of the 2545 enrolled, 93.4% were male. Compared with cohort IDU, trial IDU were younger (mean age: 28.8 versus 31.3 years), better educated (secondary level or higher: 67.2% versus 58.7%), and less likely to inject drugs daily (39.4% versus 90.4%); they were more likely to have been incarcerated (78.4% versus 65.7%), have recently injected stimulants (14.8% versus 5.8%) and tranquilizers (11.5% versus 2.3%), and obtained needles/syringes from a source other than a pharmacist (7.2% versus 3.9%) (all P ⩽ 0.003). Conclusions: IDU at high risk for HIV have been successfully enrolled in the AIDSVAX®B/E efficacy trial. Only minor epidemiologic differences were found at enrollment between trial and preparatory cohort IDU. The latter has proven critical in guiding trial design; results are expected in late 2003.
Incidence and duration of hospitalizations among persons with AIDS: an event history approach.

OBJECTIVE To analyze hospitalization patterns of persons with AIDS (PWAs) in a multi-state/multi-episode continuous time duration framework. DATA SOURCES PWAs on Medicaid identified through a match between the state's AIDS Registry and Medicaid eligibility files; hospital admission and discharge dates identified through Medicaid claims. STUDY DESIGN Using a Weibull event history framework, we model the hazard of transition between hospitalized and community spells, incorporating the competing risk of death in each of these states. Simulations are used to translate these parameters into readily interpretable estimates of length of stay, the probability that a hospitalization will end in death, and the probability that a nonhospitalized person will be hospitalized within 90 days. PRINCIPAL FINDINGS In multivariate analyses, participation in a Medicaid waiver program offering case management and home care was associated with hospital stays 1.3 days shorter than for nonparticipants. African American race and Hispanic ethnicity were associated with hospital stays 1.2 days and 1.0 day longer than for non-Hispanic whites; African Americans also experienced more frequent hospital admissions. Residents of the high-HIV-prevalence area of the state had more frequent admissions and stays two days longer than those residing elsewhere in the state. Older PWAs experienced less frequent hospital admissions but longer stays, with hospitalizations of 55-year-olds lasting 8.25 days longer than those of 25-year-olds. CONCLUSIONS Much socioeconomic and geographic variability exists both in the incidence and in the duration of hospitalization among persons with AIDS in New Jersey. Event history analysis provides a useful statistical framework for analysis of these variations, deals appropriately with data in which duration of observation varies from individual to individual, and permits the competing risk of death to be incorporated into the model. Transition models of this type have broad applicability in modeling the risk and duration of hospitalization in chronic illnesses.
A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines*

Mass spectrometry-based proteomics increasingly relies on relative or absolute quantification. In relative quantification, stable isotope based methods often allow mixing at early stages of sample preparation, whereas for absolute quantification this has generally required recombinant expression of full length, labeled protein standards. Here we make use of a very large library of Protein Epitope Signature Tags (PrESTs) that has been developed in the course of the Human Protein Atlas Project. These PrESTs are expressed recombinantly in E. coli and they consist of a short and unique region of the protein of interest as well as purification and solubility tags. We first quantify a highly purified, stable isotope labeling of amino acids in cell culture (SILAC)-labeled version of the solubility tag and use it determine the precise amount of each PrEST by its SILAC ratios. The PrESTs are then spiked into cell lysates and the SILAC ratios of PrEST peptides to peptides from endogenous target proteins yield their cellular quantities. The procedure can readily be multiplexed, as we demonstrate by simultaneously determining the copy number of 40 proteins in HeLa cells. Among the proteins analyzed, the cytoskeletal protein vimentin was found to be most abundant with 20 million copies per cell, while the transcription factor and oncogene FOS only had 6000 copies. Direct quantification of the absolute amount of single proteins is possible via a SILAC experiment in which labeled cell lysate is mixed both with the heavy labeled solubility tag and with the corresponding PrEST. The SILAC-PrEST combination allows accurate and streamlined quantification of the absolute or relative amount of proteins of interest in a wide variety of applications.
A robust heart sound segmentation algorithm for commonly occurring heart valve diseases

The first step towards detection of valvular heart diseases from heart sound signal (phonocardiogram) is segmentation. A segmentation algorithm provides the location of the first and second heart sounds which in turn helps to locate and analyse the murmur. Established phonocardiogram based segmentation methods use an electrocardiographic (ECG) signal as a continuous auxiliary input in a complex instrumentation setup. This paper proposes an automatic segmentation method that does not require any such auxiliary signal. Compared to other approaches without auxiliary signal, this work extensively utilizes biomedical domain features for reduction of time and computational complexities and is more accurate. The performance of the algorithm is evaluated for nine commonly occurring pathological cases and normal heart sound for various sampling frequencies, recording environments and age group of subjects. The proposed algorithm yields an overall accuracy of 97.47% and is compared with two competing techniques. In addition, the robustness of the algorithm is shown against additive white Gaussian noise contamination at various SNR levels.
Synthesis of internal labeled standards of melatonin and its metabolite N1‐acetyl‐N2‐formyl‐5‐methoxykynuramine for their quantification using an on‐line liquid chromatography–electrospray tandem mass spectrometry system

Abstract: Melatonin (N‐acetyl‐5‐methoxytryptamine) is implicated in physiologic changes related to light–dark cycles and has been recently found to display antioxidant properties. It is known that the reaction of melatonin with certain reactive oxygen and nitrogen species, such as hydrogen peroxide and singlet oxygen, produces N1‐acetyl‐N2‐formyl‐5‐methoxykynuramine (AFMK). We report herein on the development of a new liquid chromatography/tandem mass spectrometry (LC/ESI/MS‐MS) assay to quantitatively determine melatonin and AFMK. The stable isotopic internal standard of melatonin‐D3 was synthesized by the reaction of 5‐methoxytryptamine with deuterated acetyl chloride (CD3COCl). Labeled AFMK (AFMK‐D3) was obtained after photooxidation of melatonin‐D3. The predominant ion [M + H]+ in the full scan mass spectra of melatonin, melatonin‐D3, AFMK and AFMK‐D3 were located, respectively, at m/z = 233, 236, 265 and 268. The collision‐induced dissociation of the molecules revealed a predominant fragment at m/z = 174 for melatonin and melatonin‐D3 (loss of the N‐acetyl group), and at m/z = 178 for AFMK and AFMK‐D3 (loss of both the N‐acetyl and the N‐formyl groups). The m/z transitions from 233 to 174 (melatonin), from 236 to 174 (melatonin‐D3), from 265 to 178 (AFMK), and from 268 to 178 (AFMK‐D3) were therefore chosen for the multiple reaction monitoring detection experiments, ensuring a high specificity and an accurate quantification of melatonin and AFMK in human plasma.