Miracle-dz/UniFAR-FTUs huggingface dataset:
Catecholate Siderophores Protect Bacteria from Pyochelin Toxicity

Background Bacteria produce small molecule iron chelators, known as siderophores, to facilitate the acquisition of iron from the environment. The synthesis of more than one siderophore and the production of multiple siderophore uptake systems by a single bacterial species are common place. The selective advantages conferred by the multiplicity of siderophore synthesis remains poorly understood. However, there is growing evidence suggesting that siderophores may have other physiological roles besides their involvement in iron acquisition. Methods and Principal Findings Here we provide the first report that pyochelin displays antibiotic activity against some bacterial strains. Observation of differential sensitivity to pyochelin against a panel of bacteria provided the first indications that catecholate siderophores, produced by some bacteria, may have roles other than iron acquisition. A pattern emerged where only those strains able to make catecholate-type siderophores were resistant to pyochelin. We were able to associate pyochelin resistance to catecholate production by showing that pyochelin-resistant Escherichia coli became sensitive when biosynthesis of its catecholate siderophore enterobactin was impaired. As expected, supplementation with enterobactin conferred pyochelin resistance to the entE mutant. We observed that pyochelin-induced growth inhibition was independent of iron availability and was prevented by addition of the reducing agent ascorbic acid or by anaerobic incubation. Addition of pyochelin to E. coli increased the levels of reactive oxygen species (ROS) while addition of ascorbic acid or enterobactin reduced them. In contrast, addition of the carboxylate-type siderophore, citrate, did not prevent pyochelin-induced ROS increases and their associated toxicity. Conclusions We have shown that the catecholate siderophore enterobactin protects E. coli against the toxic effects of pyochelin by reducing ROS. Thus, it appears that catecholate siderophores can behave as protectors of oxidative stress. These results support the idea that siderophores can have physiological roles aside from those in iron acquisition.
An unusual distribution of the kdr gene among populations of Anopheles gambiae on the island of Bioko, Equatorial Guinea

In West Africa, Anopheles gambiae exists in discrete subpopulations known as the M and S molecular forms. Although these forms occur in sympatry, pyrethroid knock‐down resistance (kdr) is strongly associated with the S molecular form. On the island of Bioko, Equatorial Guinea we found high frequencies of the kdr mutation in M form individuals (55.8%) and a complete absence of kdr in the S form. We also report the absence of the kdr allele in M and S specimens from the harbour town of Tiko in Cameroon, representing the nearest continental population to Bioko. The kdr allele had previously been reported as absent in populations of An. gambiae on Bioko. Contrary to earlier reports, sequencing of intron‐1 of this sodium channel gene revealed no fixed differences between M form resistant and susceptible individuals. The mutation may have recently arisen independently in the M form on Bioko due to recent and intensive pyrethroid application.
Cardiac effects of continuous and bilevel positive airway pressure for patients with heart failure and obstructive sleep apnea: a pilot study.

BACKGROUND Obstructive sleep apnea (OSA) is prevalent in patients with heart failure. Treatment with continuous positive airway pressure (CPAP) improves systolic function in patients with heart failure. Bilevel positive airway pressure (PAP) is another treatment modality for OSA. The intermediate-term effect of bilevel PAP on left ventricular ejection fraction (LVEF) in patients with stable heart failure and OSA has not been compared to the effect of CPAP. METHODS In this pilot randomized controlled trial, patients with stable systolic dysfunction and newly diagnosed OSA (n = 24) were randomized to receive either CPAP or bilevel PAP. Titration was done in the sleep laboratory using a CPAP-based algorithm. Primary outcome was the improvement in LVEF after 3 months of treatment. Other measurements included 6-min walk test, Epworth sleepiness scale score, and the Minnesota Living With Heart Failure questionnaire. RESULTS Bilevel PAP increased LVEF 7.9% (LVEF percentage scale) more than CPAP (95% confidence interval [CI], 2.3 to 13.4; p = 0.01). In the bilevel PAP group, LVEF increased 8.5% (95% CI, 3.7 to 13.4; p = 0.002). In the CPAP group, LVEF did not change significantly (0.5%; 95% CI, - 2.7 to 3.7; p = 0.7). The difference in LVEF improvement between the two groups was still significant after adjustment for adherence, level of treatment positive pressure, body mass index, and severity of OSA. CONCLUSION This pilot randomized controlled trial suggests that bilevel PAP is superior to CPAP in improving LVEF in patients with systolic dysfunction and OSA. Larger trials are required to evaluate the mechanism behind this effect.
Clinical Correlates and Repetition of Self-Harming Behaviors Among Female Adolescent Victims of Sexual Abuse

ABSTRACT This study investigated self-harming behaviors in 149 female adolescent victims of sexual abuse, first, by determining the rates of nine types of self-mutilating behavior at intake and nine months later and, second, by investigating comorbidity of clinical correlates associated with these behaviors. The adolescents were divided into three groups according to level of self-mutilating behavior and then compared on symptom self-reports; 62.1% of the adolescents engaged in at least one self-mutilating behavior. A graded relation was observed between level of self-mutilating behavior and rate, and total number of clinical disorders. At nine month follow-up, one in four teenagers still reported a moderate or high level of self-harm. The need for systematic assessment and intervention of self-mutilating behaviors is discussed.
PerforatedCNNs: Acceleration through Elimination of Redundant Convolutions

We propose a novel approach to reduce the computational cost of evaluation of convolutional neural networks, a factor that has hindered their deployment in low-power devices such as mobile phones. Inspired by the loop perforation technique from source code optimization, we speed up the bottleneck convolutional layers by skipping their evaluation in some of the spatial positions. We propose and analyze several strategies of choosing these positions. We demonstrate that perforation can accelerate modern convolutional networks such as AlexNet and VGG-16 by a factor of 2x - 4x. Additionally, we show that perforation is complementary to the recently proposed acceleration method of Zhang et al. [28].
CRISP: Congestion reduction by iterated spreading during placement

Dramatic progress has been made in algorithms for placement and routing over the last 5 years, with improvements in both speed and quality. Combining placement and routing into a joint optimization has also been proposed. However, it remains unclear if the benefits would be significant enough to justify major changes in commercial tools. CRISP addresses this challenge and is the first tool to demonstrate tangible benefits of combined place-and-route optimization including fewer global routing detours, reduced detailed routing violations and runtime, and even shrinking the floorplan of a commercial design. We employ fast global routing to choose standard cells to temporarily inflate and iteratively spread for congestion reduction. Spreading only in congested regions, we enable die area reduction by facilitating routing with high area utilization.
Pipelined Bus-Invert Coding for FPGAs Driving High-Speed DDR-Channels

We present designs for high-speed bus-invert coding on FPGAs. The purpose is to reduce switching activities on off-chip buses driven through dual-data-rate outputs. For bus-invert coding, the performance-limiting unit is the majority voter circuit. In order to support very high data rates, we use both pipelined and approximate solutions for this unit. The approximate solution is optimized for LUT-based FPGAs and achieves high performance at lower hardware costs, at an only slightly decreased efficiency. We give performance figures for the algorithms and the circuitry.
Salbutamol via Metered-Dose Inhaler With Spacer Versus Nebulization for Acute Treatment of Pediatric Asthma in the Emergency Department

Objectives: To assess the effectiveness of salbutamol delivered via a metered-dose inhaler with spacer versus a nebulizer for acute asthma treatment in the pediatric emergency department. Methods: All consecutive children younger than 14 years old who required treatment of acute asthma exacerbation in the emergency department during May 2002 (prospective cohort, n = 321) and May 2001(retrospective cohort, n = 259) were included. Inhaled salbutamol was administered by metered-dose inhaler with a spacer (and a face mask in children younger than 2 years old) in the prospective cohort and by nebulizer in the retrospective cohort. Results: There were no significant differences between the two cohorts in the mean (±SD) age (44.50 ± 38.64 vs. 48.37 ± 43.55 months) and asthma treatment, arterial oxygen saturation (96.34 ± 2.12% vs. 96.19 ± 6.32%), and heart rate (123.71 ± 23.63 vs. 129.41 ± 34.55 beats/min) before emergency department consultation. The number of doses of inhaled bronchodilators was also similar (1.42 ± 1.01 vs. 1.45 ± 0.98) as well as the number of children that required a stay in the observation unit, admission to the hospital, or returned for medical care. The overall mean length of stay in the emergency department was slightly shorter in the prospective cohort (82 ± 48 vs. 89 ± 52 minutes). Conclusions: The administration of bronchodilators using a metered-dose inhaler with spacer is an effective alternative to nebulizers for the treatment of children with acute asthma exacerbations in the emergency department.
Cell-cycle-dependent polar morphogenesis in Caulobacter crescentus: roles of phospholipid, DNA, and protein syntheses

During swarmer cell differentiation in Caulobacter crescentus, morphogenesis at the swarmer pole is characterized by the loss of the flagellum, by the loss of phage receptor activity (PRA) (the ability of the cell to adsorb phage phi CbK), and finally by the initiation of stalk outgrowth at the site formerly occupied by the flagellum and the PRA. We show here that each of these events is a cell cycle-dependent event requiring continuous protein synthesis for its execution but occurring normally in the absence of DNA synthesis or phospholipid synthesis. During stalked-cell differentiation, the flagellum and PRA reappear and the stalk elongates considerably. We show here that these events are also cell cycle dependent, requiring not only de novo protein synthesis but also DNA and phospholipid syntheses. When synchronous cells dividing 160 min after collection were used, PRA reappearance occurred at 110 min. This PRA reappearance was dependent on a phospholipid synthesis-requiring event occurring at 70 min, a DNA synthesis-requiring event occurring at 95 min, and a protein synthesis-requiring event occurring at 108 min. In the absence of net phospholipid synthesis, stalk elongation appeared more or less normal, but the stalks eventually became fragile, and by 240 min, most of the stalks had broken off, leaving only stubs attached to the cell body.
Synthesis of ZnO Nanoparticles to Fabricate a Mask-Free Thin-Film Transistor by Inkjet Printing

We report a low-cost, mask-free, reduced material wastage, deposited technology using transparent, directly printable, air-stable semiconductor slurries and dielectric solutions. We have demonstrate an emerging process for fabricating printable transistors with ZnO nanoparticles as the active channel and poly(4-vinylphenol) (PVP) matrix as the gate dielectric, respectively, and the inkjet-printed ZnO TFTs have shown to exhibit the carrier mobility of 0.69 cm2/Vs and the threshold voltage of 25.5 V. We suggest that the printable materials and the printing technology enable the use of all-printed low-cost flexible displays and other transparent electronic applications.
Partition refinement for bisimilarity in CCP

Saraswat's concurrent constraint programming (ccp) is a mature formalism for modeling processes (or programs) that interact by telling and asking constraints in a global medium, called the store. Bisimilarity is a standard behavioural equivalence in concurrency theory, but a well-behaved notion of bisimilarity for ccp has been proposed only recently. When the state space of a system is finite, the ordinary notion of bisimilarity can be computed via the well-known partition refinement algorithm, but unfortunately, this algorithm does not work for ccp bisimilarity. In this paper, we propose a variation of the partition refinement algorithm for verifying ccp bisimilarity. To the best of our knowledge this is the first work providing for the automatic verification of program equivalence for ccp.
Crack initiation and propagation behaviour of a heat-treated carbon steel in corrosion fatigue

— When estimating fatigue damage quantitatively it is important to clarify its physical basis. In this study, rotating bending fatigue tests of a heat-treated 0.45% carbon steel were carried out in 3% NaCl solution, in order to clarify the physical basis of corrosion fatigue damage from successive observations of plastic replicas. The results show that corrosion pits are generated during the early stages of cycling, then most of them grow with further cycling until a crack is initiated from each corrosion pit. The initiation of corrosion pits from slip bands is observed only in the case when the stress range is relatively large, and in the range of stress for which slip bands are produced in air. After initiation of a crack, the crack propagates by frequent interactions and coalescence with other cracks. The growth rate of an especially small crack in NaCl solution is larger than that in air. However, the growth rate of a comparatively large crack is smaller in NaCl solution than in air.
Wavelets and Filter Banks

Wavelet and short-time Fourier analysis is introduced in the context of frequency decompositions. Wavelet type frequency decompositions are associated with lter banks, and using this fact, lter bank theory is used to construct multiplicity M wavelet frames and tight frames. The way in which lter banks lead to decomposition and recomposition of arbitrary separable Hilbert spaces is also described. E cient computational structures for both lter banks and wavelets are also discussed. Contact Address: Ramesh A. Gopinath Department of EE, A235 Rice University, Houston, TX-77251 Phone (713) 527-8750 x3577 email: ramesh@rice.edu This work was supported by AFOSR under grant 90-0334 funded by DARPA Appears in Wavelets: A Tutorial in Theory and Applications, ed. C.K. Chui, Academic Press WAVELETS AND FILTER BANKS R.A. Gopinath and C.S. Burrus Department of Electrical and Computer Engineering, Rice University, Houston, TX-77251 CML TR-91-20 30th September '91
Identification of amino acid sequences in the integrin beta 1 cytoplasmic domain implicated in cytoskeletal association

Wild-type and mutant chicken integrin beta 1 subunit (beta 1c) cDNAs were expressed in NIH 3T3 cells and assayed for localization in focal adhesions of cells plated on fibronectin substrates. Focal adhesion localization in stable transfected cells was assayed by indirect immunofluorescent staining with chicken-specific anti-beta 1c antibodies. Mutant beta 1c integrins containing internal deletions of 13 amino acids adjacent to the membrane, delta 759-771, and 20 centrally located amino acids, delta 771-790, localized in focal adhesions demonstrating that sequences required for direction to focal adhesion structures were not limited to one region of the cytoplasmic domain. Point mutations revealed three clusters of amino acids which contribute to localization in focal adhesions. These three clusters or signals are: cyto-1 (764-774), cyto-2 (785-788), and cyto-3 (797-800). The 11-residue cyto-1 signal is only found on integrin beta subunit sequences, except beta 4. Four residues within this region, D764, F768, F771, and E774, could not be altered without reducing focal adhesion staining intensities, and likely form a signal that occupies one side of an alpha helix. Mutations involving two cyto-1 residues, K770 and F771, also appeared to affect heterodimer affinity and specificity. Cyto-2 (785-788,), NPIY, is an NPXY signal that forms a tight turn motif. Cyto-2 provides a structural conformation, which when perturbed by proline removal or addition, inhibits integrin localization in focal adhesions. Cyto-3 (797-800), NPKY, resembles cyto-2, however, the nonconserved proline residue can be replaced without alteration of the localization phenotype. Cyto-3, therefore, constitutes a unique integrin signal, NXXY. Both serine and tyrosine residues at positions 790 and 788, respectively, which have been implicated in integrin phosphorylation/regulation, were conservatively replaced without detectable effect on focal adhesion localization. However, acidic replacements for these amino acids reduced focal adhesion staining intensities, suggesting that phosphorylation at these sites may negatively regulate integrin function.
The effects of Lactobacillus strains and oat fiber on methotrexate-induced enterocolitis in rats.

BACKGROUND & AIMS Administration of methotrexate to rats on an elemental diet results in severe enterocolitis and death. Lactobacilli, an integral part of the healthy gastrointestinal microecology, may provide therapeutic benefits to help the recovery from enterocolitis. The purpose of this study was to evaluate the effects of lactobacilli and oatbase on methotrexate-induced enterocolitis in rats. METHODS Rats received continuous intragastric infusion of elemental diet or with supplementation of oatbase, Lactobacillus reuteri R2LC, and Lactobacillus plantarum DSM 9843, with and without fermentation, from the beginning of the study. Methotrexate (20 mg/kg) was injected intraperitoneally on day 3, and the sampling was performed on day 6. RESULTS Lactobacilli and oatbase decreased body weight loss and intestinal permeability and increased bowel mucosal mass in enterocolitic rats. Administration of lactobacilli, but not oatbase, decreased the intestinal myeloperoxidase level, reestablished intestinal microecology, and reduced bacterial translocation to extraintestinal sites. Both lactobacilli and oatbase reduced plasma endotoxin levels. The effects of lactobacilli were greater with fermentation than without fermentation or oatbase alone, and L. plantarum was more effective in reducing intestinal pathogens than L. reuteri. CONCLUSIONS Exogenous administration of lactobacilli, especially L. plantarum with fermentation, is helpful in reducing the severity of enterocolitis in rats.
Factors affecting adoption, implementation fidelity, and sustainability of the Redesigned Community Health Fund in Tanzania: a mixed methods protocol for process evaluation in the Dodoma region

Background Despite the implementation of various initiatives to address low enrollment in voluntary micro health insurance (MHI) schemes in sub-Saharan Africa, the problem of low enrollment remains unresolved. The lack of process evaluations of such interventions makes it difficult to ascertain whether their poor results are because of design failures or implementation weaknesses. Objective In this paper, we describe a process evaluation protocol aimed at opening the ‘black box’ to evaluate the implementation processes of the Redesigned Community Health Fund (CHF) program in the Dodoma region of Tanzania. Design The study employs a cross-sectional mixed methods design and is being carried out 3 years after the launch of the Redesigned CHF program. The study is grounded in a conceptual framework which rests on the Diffusion of Innovation Theory and the Implementation Fidelity Framework. The study utilizes a mixture of quantitative and qualitative data collection tools (questionnaires, focus group discussions, in-depth interviews, and document review), and aligns the evaluation to the Theory of Intervention developed by our team. Quantitative data will be used to measure program adoption, implementation fidelity, and their moderating factors. Qualitative data will be used to explore the responses of stakeholders to the intervention, contextual factors, and moderators of adoption, implementation fidelity, and sustainability. Discussion This protocol describes a systematic process evaluation in relation to the implementation of a reformed MHI. We trust that the theoretical approaches and methodologies described in our protocol may be useful to inform the design of future process evaluations focused on the assessment of complex interventions, such as MHI schemes.
ABCB1 polymorphisms are associated with clozapine plasma levels in psychotic patients.

AIMS ABCB1 is a transmembrane transporter that is expressed in excretory organs (kidneys and liver), in intestine mucosa and on the blood-brain barrier. Because of the particular distribution of the protein, the activity of ABCB1 may significantly affect drug pharmacokinetics during absorption and distribution. Of note, several SNPs of ABCB1 are known and many of them affect transporter activity and/or expression. In this view, changes in the pharmacokinetics of drugs that are ABCB1 substrates could be clinically relevant and the evaluation of ABCB1 SNPs should deserve particular attention. Therefore, the aim of the present study was to investigate the possible association between ABCB1 polymorphisms and clozapine plasma levels in psychotic patients. MATERIALS & METHODS c.1236C>T (exon 12), c.2677G>T (exon 21) and c.3435C>T (exon 26) SNPs of ABCB1 were evaluated by PCR techniques, while plasma levels of clozapine and norclozapine were measured by HPLC in 40 men (aged, 47.6 +/- 16.6 years, median: 42 years) and 20 women (aged 40.7 +/- 11.4 years, median: 38 years) 1 month after the start of clozapine administration. RESULTS A total of three SNPs were in Hardy-Weinberg equilibrium, with a calculated frequency of the wild-type alleles of 0.54, 0.55 and 0.45 for SNPs on exons 12, 21 and 26, respectively. Patients with c.3435CC or c.2677GG genotypes had significantly lower dose-normalized clozapine levels than those who were heterozygous or TT carriers. More interestingly, c.3435CC patients (15 subjects) needed significantly higher daily doses of clozapine (246 +/- 142 mg/day) compared with the remaining 24 CT and 21 TT patients (140 +/- 90 mg/day) in order to achieve the same clinical benefit. CONCLUSION c.3435CC patients require higher clozapine doses to achieve the same plasma concentrations as CT or TT patients, and ABCB1 genotyping should be considered as a novel strategy that should improve drug use.