Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for DNA binding and multimerization

OxyR is a LysR-type transcriptional regulator which negatively regulates its own expression and positively regulates the expression of proteins important for the defense against hydrogen peroxide in Escherichia coli and Salmonella typhimurium. Using random mutagenesis, we isolated six nonrepressing OxyR mutants that were impaired in DNA binding. Five of the mutations causing the DNA binding defect mapped near the N-terminal helix-turn-helix motif conserved among the LysR family members, confirming that this region is a DNA binding domain in OxyR. The sixth nonrepressing mutant (with E-225 changed to K [E225K]) was found to be predominantly dimeric, in contrast to the tetrameric wild-type protein, suggesting that a C-terminal region defined by the E225K mutation is involved in multimerization.
Interaural Coherence and Localization

In a study of the relationship between interaural coherence and localization ability, two experiments were performed. Both made use of a 1/3 octave band of low frequency sound and a 1/3 octave band of high frequency sound. Stimuli with coherences ranging from 0.2 to 0.8 were created in three recording environments using a KEMAR and digitally altered to eliminate interaural level differences (ILD). The environments had short, medium, and long reverberation times. The coherences were measured and were accurate to one significant figure. Experiment 1 had two goals: to determine the relationship between interaural coherence and the ability to localize using interaural time differences (ITD) and to determine if localization ability was dependent only on coherence. The relationship between coherence and localization was tested in a headphone lateralization experiment in which psychometric functions were generated. The functions revealed a linear relationship, with the ability to localize high coherence sounds breaking down quickly at small ITD. Within standard error, ITD localization appeared to be dependent only on coherence. In Experiment 2, a 3-down 1-up staircase method was employed to determine how opposing ILDs affected ITD localization. When the task could be completed, the threshold values were linearly related, however, the ability broke down at large ILDs. Both experiments provide a linear description of interaural coherence and localization, with thresholds being sharp deviations from these trends.
Intramedullary Nailing for Diaphyseal Forearm Fractures in Children after Failed Conservative Treatment

Purpose. To evaluate treatment outcomes after intramedullary nailing using Ender nails for diaphyseal forearm fractures. Methods. 11 male and 9 female patients aged 6 to 15 (mean, 12) years underwent intramedullary nailing using Ender nails plus cast immobilisation for fractures of both the radius and ulna after conservative treatment had failed. Results. After a mean follow-up of 24 (range, 12–30) months, results were excellent in 14 patients, good in 5, and fair in one. None was poor. The mean operating time was 36 minutes. The mean time to bone union was 10 (range, 7–12) weeks. The mean time in the cast was 6 (range, 4–11) weeks. The mean time to implant removal was 8 (range, 6–10) months. All patients regained a full range of elbow movement, except in one who had limited supination and pronation (<20°) due to a degree of malrotation. Two patients had pain owing to nail protrusion. One patient had a superficial infection. One patient had transient neurapraxia. Conclusion. Intramedullary nailing using Ender nails plus cast immobilisation is effective for diaphyseal forearm fractures in children after conservative treatment has failed.
Frequency tunable directive antenna by ferromagnetic photonic crystals

We theoretically and experimentally demonstrate that the frequency tunable directive radiation can be achieved by the current line source embedded in two dimensional magnetic photonic crystals (PC). By lowering the symmetry of the PC, the source radiation can radiate in one direction with high directivity when it operates at the band edge of the PC. The radiation frequency can be tuned in a broadband frequency range through change the magnitude of bias magnetic fields. For the magnetic PC made of MgMn ferrite and designed in microwave X-band, the source radiation has a sharp main beam and no sidelobes. The dynamic tunable frequency range is up to 2.1 GHz in which the average directivity is about 30. The directive radiation and its frequency tunability are further demonstrated by experiments.
Structure of a pancreatic α‐amylase bound to a substrate analogue at 2.03 Å resolution

The structure of pig pancreatic α‐amylase in complex with carbohydrate inhibitor and proteinaceous inhibitors is known but the successive events occurring at the catalytic center still remain to be elucidated. The X‐ray structure analysis of a crystal of pig pancreatic α‐amylase (PPA, EC 3.2.1.1.) soaked with an enzyme‐resistant substrate analogue, methyl 4,4′‐dithio‐α‐maltotrioside, showed electron density corresponding to the binding of substrate analogue molecules at the active site and at the “second binding site. ” The electron density observed at the active site was interpreted in terms of overlapping networks of oligosaccharides, which show binding of substrate analogue molecules at subsites prior to and subsequent to the cleavage site. A weaker patch of density observed at subsite ‐1 (using a nomenclature where the site of hydrolysis is taken to be between subsites ‐1 and +1) was modeled with water molecules. Conformational changes take place upon substrate analogue binding and the “flexible loop” that constitutes the surface edge of the active site is observed in a specific conformation. This confirms that this loop plays an important role in the recognition and binding of the ligand. The crystal structure was refined at 2.03 Å resolution, to an R‐factor of 16.0 (Rfree 18.5).
Psychiatry of the elderly: the WPA/WHO consensus statements

The World Psychiatric Association is a loose confederation of national psychiatric societies. It has over 50 `Sections' representing special interests within psychiatry. The main functions of the Sections are the organisation of scienti®c meetings and the development of educational material. Any educational material produced must have `world' relevance, and in particular be responsive to the needs of evolving psychiatric services in the developing world. Between 1997 and 1999, under the Chairmanship of the late Professor Jean Wertheimer, the World Psychiatric Association Section of Geriatric Psychiatry has published a series of consensus statements in collaboration with the World Health Organisation Division of Mental Health, aimed at encouraging and facilitating the development of specialist psychiatric services for older people. The ®rst Consensus Statement (WHO, 1996) de®nes the scope of the specialty, emphasising that this has become necessary because of increasing longevity (most markedly in the developing world); the relatively high prevalence both of functional mental disorders and of the dementias in old age; and the need to adopt a multidisciplinary approach while de®ning professional roles within the team. The scope of psychiatry of the elderly is `the psychiatry of `retired'' people', and includes the full range of mental illnesses, including aective disorders, psychoses, substance abuse, the dementias and the mental health problems of `graduates' whose mental health problems continue into old age. The document emphasises that the specialty also needs to address psychological, physical and social aspects of mental health problems in older people and the biosociocultural changes associated with ageing. The characteristics of a successful psychiatry service for the elderly are summarised as community orientation, a multidisciplinary approach, an emphasis on abilities as well as de®cits, and a core aim to improve quality of life rather than simply to alleviate symptoms. The main objectives of treatment are the restoration of health, improving quality of life, minimising disability, preserving autonomy and addressing the needs of family and other carers as well as those of the individual patient. The high relapse rate of functional psychiatric problems in old age necessitates close follow-up after successful initial treatment. Priorities within any new specialist service include teaching psychiatry of the elderly to primary health care workers; training existing mental health professionals in special mental health problems of the elderly; and establishing at least one multidisciplinary resource/expertise centre. The second Consensus Statement (WHO, 1997) provides a blueprint for the development of new specialist services and also serves as a checklist for assessing established services. It identi®es general principles which should underpin any quality specialist psychiatry of the elderly service:
Identification of Secreted Proteins ofMycobacterium tuberculosis by a Bioinformatic Approach

ABSTRACT Proteins secreted by Mycobacterium tuberculosis are usually targets of immune responses in the infected host. Here we describe a search for secreted proteins that combined the use of bioinformatics and phoA′ fusion technology. The 3,924 proteins deduced from the M. tuberculosis genome were analyzed with several computer programs. We identified 52 proteins carrying an NH2-terminal secretory signal peptide but lacking additional membrane-anchoring moieties. Of these 52 proteins—the TM1 subgroup—only 7 had been previously reported to be secreted proteins. Our predictions were confirmed in 9 of 10 TM1 genes that were fused to Escherichia coli phoA′, a marker of subcellular localization. These findings demonstrate that the systematic computer search described in this work identified secreted proteins of M. tuberculosis with high efficiency and 90% accuracy.
Identification of N-(Deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo [4,5-b]pyridine as the major adduct formed by the food-borne carcinogen, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine, with DNA.

The covalent binding of the N-acetoxy-, N-hydroxy-, and nitro derivatives of the food-borne carcinogen 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) to 2'-deoxyribonucleosides or DNA was investigated in vitro and in vivo. N-Acetoxy-PhIP reacted with deoxyguanosine (dG), but not with the other deoxyribonucleosides, to form N-(deoxyguanosin-8-yl)-PhIP (dG-C8-PhIP), whose structure was determined by NMR and mass spectral analyses and by ultraviolet absorption and pH-solvent partitioning characteristics. While reaction of N-acetoxy-PhIP with calf thymus DNA at pH 5.0 yielded 5.38 +/- 1.16 nmol of bound PhIP residues/mg of DNA, N-hydroxy-PhIP gave only 0.13-0.23 nmol binding/mg of DNA under identical reaction conditions. Nitro-PhIP produced no detectable binding under these conditions. HPLC analysis of 1-butanol extracts of enzymatically hydrolyzed DNA that had been modified by N-acetoxy-PhIP in vitro showed a major adduct which coeluted with and had an ultraviolet absorption and a mass spectrum that were identical to that of authentic dG-C8-PhIP. 32P-Postlabeling analysis of DNA isolated from colon, pancreas, lung, heart, and liver of rats treated orally with PhIP revealed the presence of a major PhIP-DNA adduct. This adduct had chromatographic properties identical to that of the 32P-labeled bis(phosphate) derivative of dG-C8-PhIP and represented 35-45% of the total adducts. (ABSTRACT TRUNCATED AT 250 WORDS)
Cellular, Pharmacological, and Biophysical Evaluation of Explanted Lungs from a Patient with Sickle Cell Disease and Severe Pulmonary Arterial Hypertension

Pulmonary hypertension is recognized as a leading cause of morbidity and mortality in patients with sickle cell disease (SCD). We now report benchtop phenotyping from the explanted lungs of the first successful lung transplant in SCD. Pulmonary artery smooth muscle cells (PASMCs) cultured from the explanted lungs were analyzed for proliferate capacity, superoxide (O2•–) production, and changes in key pulmonary arterial hypertension (PAH)–associated molecules and compared with non-PAH PASMCs. Upregulation of several pathologic processes persisted in culture in SCD lung PASMCs in spite of cell passage. SCD lung PASMCs showed growth factor– and serum-independent proliferation, upregulation of matrix genes, and increased O2•– production compared with control cells. Histologic analysis of SCD-associated PAH arteries demonstrated increased and ectopically located extracellular matrix deposition and degradation of elastin fibers. Biomechanical analysis of these vessels confirmed increased arterial stiffening and loss of elasticity. Functional analysis of distal fifth-order pulmonary arteries from these lungs demonstrated increased vasoconstriction to an α1-adrenergic receptor agonist and concurrent loss of both endothelial-dependent and endothelial-independent vasodilation compared with normal pulmonary arteries. This is the first study to evaluate the molecular, cellular, functional, and mechanical changes in end-stage SCD-associated PAH.
Convex surface decomposition

This video, which is basedon [I], illustrates heuristics for decomposing the boundary of a polyhedron into convex-shaped pieces. The problem is NPcomplete, so heuristics are the best one can (probably) expect. The problem is motivated by applications in manufacturing, computer graphics, multimedia systems, etc. Finding meaningful test data was an important component of this work. We collected several hundred real-life polyhedral models from manufacturing companies and industrial AutoCAD users. The first part of the video displays a sample of these objects (e.g., Figure 1).
Ultrastructure of stomatal development in early-divergent angiosperms reveals contrasting patterning and pre-patterning.

BACKGROUND AND AIMS Angiosperm stomata consistently possess a pair of guard cells, but differ between taxa in the patterning and developmental origin of neighbour cells. Developmental studies of phylogenetically pivotal taxa are essential as comparative yardsticks for understanding the evolution of stomatal development. METHODS We present a novel ultrastructural study of developing stomata in leaves of Amborella (Amborellales), Nymphaea and Cabomba (Nymphaeales), and Austrobaileya and Schisandra (Austrobaileyales), representing the three earliest-divergent lineages of extant angiosperms (the ANITA-grade). KEY RESULTS Alternative developmental pathways occur in early-divergent angiosperms, resulting partly from differences in pre-patterning and partly from the presence or absence of highly polarized (asymmetric) mitoses in the stomatal cell lineage. Amplifying divisions are absent from ANITA-grade taxa, indicating that ostensible similarities with the stomatal patterning of Arabidopsis are superficial. In Amborella, 'squared' pre-patterning occurs in intercostal regions, with groups of four protodermal cells typically arranged in a rectangle; most guard-mother cells are formed by asymmetric division of a precursor cell (the mesoperigenous condition) and are typically triangular or trapezoidal. In contrast, water-lily stomata are always perigenous (lacking asymmetric divisions). Austrobaileya has occasional 'giant' stomata. CONCLUSIONS Similar mature stomatal phenotypes can result from contrasting morphogenetic factors, although the results suggest that paracytic stomata are invariably the product of at least one asymmetric division. Loss of asymmetric divisions in stomatal development could be a significant factor in land plant evolution, with implications for the diversity of key structural and physiological pathways.
Psychosocial interventions for suicidal children and adolescents

This paper discusses the role of psychosocial intervention in the treatment of suicidal youth, summarizes the existing relevant literature, describes model programs for treating suicidal youth, and discusses efficacy‐to‐effectiveness issues in working with this population. Depression and Anxiety 14:192–197, 2001. © 2001 Wiley‐Liss, Inc.
Ethical Dilemmas for Adaptive Persuasion Systems

A key acceptability criterion for artificial agents will be the possible moral implications of their actions. In particular, intelligent persuasive systems (systems designed to influence humans via communication) constitute a highly sensitive topic because of their intrinsically social nature. Still, ethical studies in this area are rare and tend to focus on the output of the required action; instead, this work focuses on the acceptability of persuasive acts themselves.Building systems able to persuade while being ethically acceptable requires that they be capable of intervening flexibly and of taking decisions about which specific persuasive strategy to use. We show how, exploiting a behavioral approach, based on human assessment of moral dilemmas, we obtain results that will lead to more ethically appropriate systems. Experiments we have conducted address the type of persuader, the strategies adopted and the circumstances. Dimensions surfaced that can characterize the interpersonal differences concerning moral acceptability of machine performed persuasion, usable for strategy adaptation. We also show that the prevailing preconceived negative attitude toward persuasion by a machine is not predictive of actual moral acceptability judgement when subjects are confronted with specific cases.
Neoadjuvant Paclitaxel Poliglumex, Cisplatin, and Radiation for Esophageal Cancer: A Phase 2 Trial

PurposeTo evaluate the pathologic complete response (CR) rate and safety of paclitaxel poliglumex (PPX), cisplatin, and concurrent radiation for patients with esophageal cancer. Patients and MethodsPatients with adenocarcinoma or squamous cell carcinoma of the esophagus or gastroesophageal junction with no evidence of distant metastasis received PPX (50 mg/m2/wk) and cisplatin (25 mg/m2/wk) for 6 weeks with 50.4 Gy concurrent radiation. Six to eight weeks after completion of chemoradiotherapy, patients underwent surgical resection. ResultsForty patients were enrolled, 37 patients with adenocarcinoma and 3 patients with squamous cell cancer. The treatment-related grade 3 nonhematologic toxicities included esophagitis (7%), nausea (7%), and fatigue (5%). Three patients with clinical endoscopic CR (2 with squamous cell cancer) refused surgery. Twelve of the remaining 37 patients (32%) had a pathologic CR. The 12 patients with pathologic CR all had adenocarcinoma. ConclusionPPX, cisplatin, and concurrent radiation are well tolerated, easily administered regimen for esophageal cancer with a low incidence of significant esophagitis and a high pathologic CR rate consistent with the preclinical data of PPX and radiation.
Update: human papillomavirus infection remains highly prevalent and persistent among HIV-infected individuals

Purpose of review Human papillomavirus infections and human papillomavirus-associated anogenital tumors are more prevalent in HIV-infected than HIV-uninfected individuals. This review focuses on recent developments related to human papillomavirus burden in HIV-infected individuals; anogenital human papillomavirus types and type-specific differences in the natural history of human papillomavirus infections; the effect of highly active antiretroviral therapy on human papillomavirus infection; and novel human papillomavirus therapeutic interventions. Recent findings There is a paucity of recent data on the effect of highly active antiretroviral therapy on human papillomavirus infection and its related anogenital abnormalities/cancer. Review articles on the molecular biology of human papillomavirus in HIV infection outline why, despite highly active antiretroviral therapy, anogenital tumors may continue to increase in this population. Studies continue to confirm the high prevalence of human papillomavirus infection and to define the different human papillomavirus types correlated with anogenital cytologic abnormalities, an important area in light of the development of an effective type-specific human papillomavirus vaccine. Summary Anogenital human papillomavirus infection remains highly prevalent and persistent in HIV-infected individuals. HIV is associated with a wide diversity of human papillomavirus types and a high prevalence of anogenital cytologic abnormalities. The incidence of anogenital human papillomavirus-related cancers remains high in the highly active antiretroviral therapy era, raising concerns of human papillomavirus infections as a rising health burden among HIV-infected individuals. Interventions aimed at preventing human papillomavirus infections with vaccinations need to be evaluated in HIV-infected individuals.
Rapid Staphylococcus aureus agr Type Determination by a Novel Multiplex Real-Time Quantitative PCR Assay

ABSTRACT The accessory gene regulator (agr) is a crucial regulatory component of Staphylococcus aureus involved in the control of bacterial virulence factor expression. We developed a real-time multiplex quantitative PCR assay for the rapid determination of S. aureus agr type. This assay represents a rapid and affordable alternative to sequence-based strategies for assessing relevant epidemiological information.
The Role of Surface Chemistry in Filter Feeding by Zooplankton

Surface chemistry of both particles and animals is important in filter feeding at low Reynolds number. Daphnia magna, fed mixtures of three sizes of polystyrene particles, retained particles that were smaller than the mesh size of the animals (1.0 micrometer) at greater efficiencies than predicted by a sieving model. Retention efficiency of the smallest particles (0.5 micrometer) was increased when negative surface charge on the particles was neutralized, and retention was decreased when a nonionic surfactant was, added to reduce wettability.
Exhaled Nitric Oxide in Relation to the Clinical Features of Childhood Asthma

Background. Exhaled nitric oxide (ENO) has been shown to be a noninvasive marker of eosinophilic inflammation in asthmatic children. Few studies have evaluated the relationship between ENO levels and the clinical features of children with asthma. The aim of this study was to examine children attending a routine asthma clinic and evaluate the relationship between ENO levels and clinical parameters including decision making. Methods. Asthmatic children (n = 133, aged 5 to 14 years) attending a hospital asthma clinic were studied. ENO levels were measured and compared between subgroups of subjects according to recent symptoms, asthma control and treatment, and the clinician's decision (blinded to ENO levels) regarding further management. Results. ENO levels (median [IQR] ppb) were significantly elevated in children who had recent symptoms compared to those without recent symptoms (14.6 [6.5 to 45.3] vs. 6.0 [3.2 to 17.4], difference between medians 8.6, 95% confidence interval [CI] (1.8 to 13.9, p = 0.004). ENO levels differed significantly between the controlled and uncontrolled subgroups (8.5 [4.2 to 26.4] vs. 26.4 [5.0 to 62.0], difference between medians 17.9, 95% CI 0.1 to 22.8, p = 0.03) and between the three treatment decision subgroups (up, down, or unchanged; p < 0.001). Conclusions. ENO levels are strongly related to the clinical features of childhood asthma and the clinical decision making process. To fully evaluate the role of ENO in the clinical management of asthma, this “proof of concept” study paves the way for prospective randomized trials of the inclusion of ENO levels in the decision making process in childhood asthma.