bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative chimeric analysis of six specificity determinants that differentiate Escherichia coli aspartate from tyrosine aminotransferase
Authors: Shaffer Wendy A. , Luong Tinh N. , Rothman Steven C. , Kirsch Jack F. 
Published: November 2002

AbstractThe six mutations, referred to as the Hex mutations, that together have been shown to convert Escherichia coli aspartate aminotransferase (AATase) specificity to be substantially like that of E. coli tyrosine aminotransferase (TATase) are dissected into two groups, (T109S/N297S) and (V39L/K41Y/T47I/N69L). The letters on the left and right of the numbers designate AATase and TATase residues, respectively. The T109S/N297S pair has been investigated previously. The latter group, the “Grease” set, is now placed in the AATase framework, and the retroGrease set (L39V/Y41K/I47T/L69N) is substituted into TATase. The Grease mutations in the AATase framework were found primarily to lower KMs for both aromatic and dicarboxylic substrates. In contrast, retroGrease TATase exhibits lowered kcats for both substrates. The six retroHex mutations, combining retroGrease and S109T/S297N, were found to invert the substrate specificity of TATase, creating an enzyme with a nearly ninefold preference (kcat/KM) for aspartate over phenylalanine. The retroHex mutations perturb the electrostatic environment of the pyridoxal phosphate cofactor, as evidenced by a spectrophotometric titration of the internal aldimine, which uniquely shows two pKas, 6.1 and 9.1. RetroHex was also found to have impaired dimer stability, with a KD for dimer dissociation of 350 nM compared with the wild type KD of 4 nM. Context dependence and additivity analyses demonstrate the importance of interactions of the Grease residues with the surrounding protein framework in both the AATase and TATase contexts, and with residues 109 and 297 in particular. Context dependence and cooperativity are particularly evident in the effects of mutations on kcat/KM(Asp). Effects on kcat/KM(Phe) are more nearly additive and context independent.
Side‐chain conformational entropy at protein–protein interfaces
Authors: Cole Christian , Warwicker Jim 
Published: November 2002

AbstractProtein–protein interactions are the key to many biological processes. How proteins selectively and correctly associate with their required protein partner(s) is still unclear. Previous studies of this “protein‐docking problem” have found that shape complementarity is a major determinant of interaction, but the detailed balance of energy contributions to association remains unclear. This study estimates side‐chain conformational entropy (per unit solvent accessible area) for various protein surface regions, using a self‐consistent mean field calculation of rotamer probabilities. Interfacial surface regions were less flexible than the rest of the protein surface for calculations with monomers extracted from homodimer datasets in 21 of 25 cases, and in 8 of 9 for the large protomer from heterodimer datasets. In surface patch analysis, based on side‐chain conformational entropy, 68% of true interfaces were ranked top for the homodimer set and 66% for the large protomer/heterodimer set. The results indicate that addition of a side‐chain entropic term could significantly improve empirical calculations of protein–protein association.
Mechanically unfolding proteins: The effect of unfolding history and the supramolecular scaffold
Authors: Zinober Rebecca C. , Brockwell David J. , Beddard Godfrey S. , Blake Anthony W. , Olmsted Peter D. , Radford Sheena E. , Smith D. Alastair 
Published: November 2002

AbstractThe mechanical resistance of a folded domain in a polyprotein of five mutant I27 domains (C47S, C63S I27)5is shown to depend on the unfolding history of the protein. This observation can be understood on the basis of competition between two effects, that of the changing number of domains attempting to unfold, and the progressive increase in the compliance of the polyprotein as domains unfold. We present Monte Carlo simulations that show the effect and experimental data that verify these observations. The results are confirmed using an analytical model based on transition state theory. The model and simulations also predict that the mechanical resistance of a domain depends on the stiffness of the surrounding scaffold that holds the domain in vivo, and on the length of the unfolded domain. Together, these additional factors that influence the mechanical resistance of proteins have important consequences for our understanding of natural proteins that have evolved to withstand force.
Prediction of novel archaeal enzymes from sequence‐derived features
Authors: Jensen Lars Juhl , Skovgaard Marie , Brunak Søren 
Published: November 2002

AbstractThe completely sequenced archaeal genomes potentially encode, among their many functionally uncharacterized genes, novel enzymes of biotechnological interest. We have developed a prediction method for detection and classification of enzymes from sequence alone (available at http://www.cbs.dtu.dk/services/ArchaeaFun/). The method does not make use of sequence similarity; rather, it relies on predicted protein features like cotranslational and posttranslational modifications, secondary structure, and simple physical/chemical properties.
Competing Commitments: Technocracy and Democracy in the Design of Monetary Institutions
Authors: Freeman John R. 
Published: November 2002

In this article, I refine and expand the agenda for research on monetary institutions. First, I evaluate the analyses and research designs presented in this special issue ofInternational Organization. Out of this evaluation, several ideas about how to produce a “third generation” of research on this topic emerge. Specific ideas include how to: create a better synthesis with certain branches of economics, such as information economics; broaden the welfare criteria on which institutional choices are made; deepen the analyses of coalitional and other political processes on which the choice of institutions are based; and strengthen the tests that are offered in support of these choices.In the second part of this article, I explore questions of how popular sovereignty over economic policy and institutional choice are achieved. I show that the institutional regimes proposed in the special issue are, in a sense, democratic as long as the public's “perceived consensus” about economic policies and macroeconomic outcomes is real. However, if, as new work suggests, there is genuine dissensus about policy and macroeconomic objectives, it is no longer clear that the regimes proposed in the special issue are democratic. In the conclusion, I briefly discuss a possible crisis of imagination in institutional design.
Association of lipid peroxidation with hepatocellular injury in preterm infants
Authors: Weinberger Barry , Watorek Kazimierz , Strauss Richard , Witz Gisela , Hiatt Mark , Hegyi Thomas 
Published: November 2002

Abstract
Introduction
We wished to determine whether cholestasis induced by total parenteral nutrition (TPN) in preterm newborn infants is associated with increased oxidative stress secondary to increased reactive oxygen intermediates. We hypothesized that elevated urinary thiobarbituric-acid-reacting substances (TBARS), a marker of oxidative stress, would be associated with hepatocellular injury as measured by serum alanine transaminase (ALT) and aspartate transaminase (AST) levels.

Materials and methods
Preterm infants (<35 weeks' gestation) admitted to the neonatal intensive care unit were enrolled (with their parents' informed consent) in either the 'cholestasis' group (if their direct bilirubin was >2 mg/dl [34.2 μmol/l] and duration of TPN was ≥ 10 days [n = 27]) or in the control group. Urine samples for measurement of TBARS (proportionate to lipid peroxidation) and blood specimens for analysis of serum bilirubin, ALT, AST, and alkaline phosphatase were obtained within 24 hours of enrollment.

Results
The cholestasis and control groups were comparable with respect to gestational age, birth weight, Apgar score, maximum FiO2, and duration of supplemental oxygen administration. Median serum direct bilirubin concentrations in the cholestasis and control groups were, respectively, 3.3 mg/dl (56.4 μmol/l) and 1.7 mg/dl (29.1 μmol/l) (P < 0.001). Serum ALT and AST levels were also elevated in the cholestasis group, but alkaline phosphatase levels did not differ significantly between the groups. Urinary levels of TBARS in all the infants were correlated with ALT and AST but did not differ significantly between cholestatic and control infants.

Discussion
Our findings suggest that oxidant stress is associated with hepatocellular injury in preterm infants. This effect is not correlated with the degree of cholestasis.
Bovine colostrum in oral treatment of enterogenic endotoxaemia in rats
Authors: Döhler J Rüdiger , Nebermann Lars 
Published: November 2002

Abstract
Introduction
Under conditions of shock, bacteria and endotoxins in the intestines can traverse the mucosal barrier by translocation and enter the blood and lymphatic system. Immunoglobulins and lactoferrin have been reported to neutralize endotoxins and bacteria. We studied the essential therapeutic factors of colostrum products in an animal experiment.

Method
We simulated endotoxaemia by per-oral administration of a suspension of Escherichia coli and antibiotics into the duodenum of anaesthetized rats after giving intraperitoneal carrageenan. At the same time, pure bovine colostrum or lactoferrin-enriched bovine colostrum was given. Therapeutic effects were studied by examining plasma endotoxin activity and bacterial contamination of mesenterial lymph nodes and peritoneal lavages. Albumin was used in a control group.

Results
The most effective bovine colostrum was able to reduce the maximum plasma endotoxin value by 67% as compared with the albumin group. The combination of this colostrum with lactoferrin brought about a reduction by 80%. The reduction in bacterial contamination of lymph nodes and peritoneal lavages was also evident.

Conclusion
Both gammaglobulin and lactoferrin may help to eliminate endotoxins when bovine colostrum is administered into the gut in conditions of septic shock.
Stress ulcer prophylaxis in trauma patients
Authors: Barletta Jeffrey F , Erstad Brian L , Fortune John B 
Published: November 2002

Abstract
Introduction
A number of issues concerning stress ulcer prophylaxis remain unresolved despite numerous randomized, controlled trials and several meta-analyses. The role of stress ulcer prophylaxis, particularly in trauma patients, is further complicated by the lack of trials utilizing clinically important bleeding as an endpoint. Given the lack of consensus regarding stress ulcer prophylaxis in trauma patients, prescribing practices at Level I trauma centers in the United States were assessed.

Materials and methods
A survey was developed that contained questions related to institutional prescribing and evaluation of stress ulcer prophylaxis. The survey was intended to delineate these practices at the 188 Level I trauma centers (at the time of the present survey) in the United States.

Results
One hundred and nineteen surveys were returned, yielding a response rate of 63%. Eighty-six percent stated that medications for stress ulcer prophylaxis are used in a vast majority of trauma patients admitted to the intensive care unit. Sixty-five percent stated that there is one preferred medication. For these institutions, histamine-2-blockers were the most popular at 71%. Thirty-nine percent stated that greater than 50% of patients remain on stress ulcer prophylaxis following discharge from the intensive care unit.

Conclusion
The lack of consensus with regards to appropriate stress ulcer prophylaxis is apparent in this survey of Level I trauma centers. For those institutions with a preferred agent, histamine-2-blockers were most common.
Ethnic differences in prisoners
Authors: Coid Jeremy , Petruckevitch Ann , Bebbington Paul , Brugha Traolach , Bhugra Dinesh , Jenkins Rachel , Farrell Mike , Lewis Glyn , Singleton Nicola 
Published: November 2002

BackgroundThe high rates of psychiatric morbidity in prisoners vary between ethnic groups.AimsTo compare early environmental risks, stressful daily living experiences and reported use of psychiatric services in prisoners from different ethnic groups.MethodCross-sectional survey of 3142 prisoners in all penal establishments in England and Wales in 1997.ResultsFewer Black and South Asian male prisoners reported childhood traumas and conduct disorder, and fewer Black prisoners experienced stressful prison experiences, than White prisoners. Fewer Black women had received previous psychiatric treatment, and fewer Black men had their psychiatric problems identified in prison. Black prisoners were less likely to have received psychiatric treatment than Whites.ConclusionsThe lower prevalence of psychiatric morbidity observed in Black prisoners corresponds with reduced exposure to risk factors. Higher rates of imprisonment might be explained by higher rates of conduct disorder, adolescent-onset criminality and disadvantage within the criminal justice system.
Post-partum depression in a cohort of women from a rural area of Tamil Nadu, India
Authors: Chandran Mani , Tharyan Prathap , Muliyil Jayaprakash , Abraham Sulochana 
Published: November 2002

BackgroundCommunity-based epidemiological data on post-partum depression from developing countries are scarce.AimsTo determine the incidence of and risk factors for developing post-partum depression in a cohort of women living in rural south India.MethodWe assessed 359 women in the last trimester of pregnancy and 6–12 weeks after delivery for depression and for putative risk factors.ResultsThe incidence of post-partum depression was 11% (95% CI 7.1–14.9). Low income, birth of a daughter when a son was desired, relationship difficulties with mother-in-law and parents, adverse life events during pregnancy and lack of physical help were risk factors for the onset of post-partum depression.ConclusionsDepression occurred as frequently during late pregnancy and after delivery as in developed countries, but there were cultural differences in risk factors. These findings have implications for policies regarding maternal and child-care programmes.
Intramolecular Mannich Reaction of 2-Oxotryptamine and Homologues with Oxo Reagents Yielding Spiro Compounds. Part II
Authors: Dörnyei Gábor , Incze Mária , Kajtár-Peredy Mária , Szántay Csaba 
Published: November 2002

2-Oxotryptamine and its homo derivative undergo intramolecular Mannich-type cyclization with acetone and other ketones to give spiro[indole-3,3'-pyrrolidin]-2-ones and spiro[indole-3,3'-piperidin]-2-ones. A similar reaction with the bis-homologue of 2-oxotryptamine to yield spiro[azepane-3,3'-indol]-2'-ones was unsuccessful.
Outcome of clinical risk management in the Gloucester
rehabilitation service
Authors: Macpherson Rob , Cornelius Faith , Kilpatrick Daphne , Blazey Kate 
Published: November 2002

Aims and MethodTo assess the impact of a clinical risk assessment and management policy
introduced in a tertiary rehabilitation service, in response to UK
government statute. The study assessed the effect of a formal risk
management approach for high-risk cases over a year, in terms of changes
in risk-associated behaviour and perceived levels of risk, and in
achievement of clinical risk management goals.ResultsInitially 35 of 107 patients were rated as high risk, mostly of neglect
or of harm to others, and were subjected to formal risk management. At
follow-up only 16 patients were still rated as high risk, most reduction
occurring in risk of neglect. Half of the 112 risk management goals
established were fully achieved, 58 partially and 18 not achieved. Total
Social Behaviour Schedule ratings were significantly lower at
follow-up.Clinical ImplicationsRisk management appeared to be successful in terms of reducing overall
levels of risk, the achievement of risk management goals and the
reduction of risk-associated behaviours. The lack of a control group and
blindness limits the validity of these findings. However, organised risk
management procedures may help to support and promote good general
clinical management.
Lelliottia
Authors: Brady Carrie L. 
Published: January 2024

Abstract

Lel.li.ot'ti.a. N.L. fem. n.
Lelliottia
, named after R.A. Lelliott for his contributions to the understanding of bacterial plant diseases.

Pseudomonadota / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Lelliottia

The genus
Lelliottia
includes species regularly isolated from water, soil, spoiled fruit and vegetables, elm trees suffering from “wetwood” disease, and also from clinical samples. Cells are Gram‐stain‐negative, facultatively anaerobic, motile rods. Species are mesophilic, favoring growth temperatures of 30–35°C. Carbon sources such as glucose, cellobiose, fructose, galactose, maltose, mannose,
N
‐acetylglucosamine, and
N
‐acetylgalactosamine are readily assimilated. Species form a monophyletic clade when phylogenetic analysis is based on multilocus sequence analysis (MLSA) or whole‐genome sequences. The major fatty acids are C
16:0
, C
17:0
cyclo, C
18:1
ω7
c
, and summed features 2 (iso‐C
16:1
and/or C
14:0
3‐OH) and 3 (C
16:1
ω7
c
and/or iso‐C
15:0
2‐OH).

DNA G + C content (mol%)
: 52.8–56.0 (genome analysis).

Type species
:
Lelliottia nimipressuralis
Brady et al. 2013, VL154 (basonym: “
Erwinia nimipressuralis
” Carter 1945).
Identification algorithm for power quality disturbance of inspection robot in converter station during operation
Authors: Zhou Xu , Zhang Rui , Li Lin , Wang Bin , Cao Xianwu 
Published: January 2024

AbstractAs power quality disturbances become increasingly complex, it is imperative that the speed and accuracy of the inspection robot at the converter station be improved. For this purpose, this study designs a power quality disturbance feature extraction method based on the fast‐adaptive S‐transform. This method preserves the main feature information and eliminates redundant calculations on the basis of adaptive transform. On this basis, a power quality disturbance identification model built on a multi label lightweight gradient elevator is constructed. In the experimental results, compared to the generalized S‐transform, adaptive S‐transform, and S‐transform, the total extraction time of the proposed method was reduced by 96.09%, 91.56%, and 91.22%, respectively. The average accuracy of extracting features for a single disturbance was 99.56%, while for complex disturbance, it was 98.24%, both of which outperformed the comparison algorithms. It is verified that the proposed method can improve the extraction accuracy of power quality disturbance signal. In the recognition of a single disturbance signal, the constructed model exhibited a high accuracy of over 99%. In recognizing composite disturbance signals, the model demonstrated high accuracy and strong stability. Its effectiveness has been confirmed through experiments. The paper aims to enhance the speed and accuracy of power quality disturbance recognition algorithms. This will assist inspection robots working in converter stations, and ensure stable and safe operation of the power grid.
Modeling of a Bioengineered Immunomodulating Microenvironment for Cell Therapy
Authors: Capuani Simone , Campa‐Carranza Jocelyn Nikita , Hernandez Nathanael , Chua Corrine Ying Xuan , Grattoni Alessandro 
Published: January 2024

AbstractCell delivery and encapsulation platforms are under development for the treatment of Type 1 Diabetes among other diseases. For effective cell engraftment, these platforms require establishing an immune‐protected microenvironment as well as adequate vascularization and oxygen supply to meet the metabolic demands of the therapeutic cells. Current platforms rely on 1) immune isolating barriers and indirect vascularization or 2) direct vascularization with local or systemic delivery of immune modulatory molecules. Supported by experimental data, here a broadly applicable predictive computational model capable of recapitulating both encapsulation strategies is developed. The model is employed to comparatively study the oxygen concentration at different levels of vascularization, transplanted cell density, and spatial distribution, as well as with codelivered adjuvant cells. The model is then validated to be predictive of experimental results of oxygen pressure and local and systemic drug biodistribution in a direct vascularization device with local immunosuppressant delivery. The model highlights that dense vascularization can minimize cell hypoxia while allowing for high cell loading density. In contrast, lower levels of vascularization allow for better drug localization reducing systemic dissemination. Overall, it is shown that this model can serve as a valuable tool for the development and optimization of platform technologies for cell encapsulation.
Discovery of Broad‐Spectrum Repurposed Drug Combinations Against Carbapenem‐ResistantEnterobacteriaceae(CRE) Through Artificial Intelligence (AI)‐Driven Platform
Authors: Li Ming , You Kui , Wang Peter , Hooi Lissa , Chen Yahua , Siah Anqi , Tan Shi‐Bei , Teo Jeanette , Ng Oon‐Tek , Marimuthu Kalisvar , Venkatachalam Indumathi , Blasiak Agata , Chow Edward Kai‐Hua , Ho Dean , Gan Yunn‐Hwen 
Published: January 2024

AbstractAntimicrobial resistance challenges the sustainability of healthcare systems and results in substantial economic losses worldwide. This issue is further aggravated by paucity of new drugs and treatment options. In this study, an artificial intelligence (AI)‐derived platform termed IDentif.AI is utilized to accelerate the development of effective therapeutic options for carbapenem‐resistantEnterobacteriaceae(CRE). Twelve Food and Drug Administration‐approved drugs are selected and the in vitro inhibitory efficacy of 155 combinations consisting of various drugs is determined at different concentrations against bothKlebsiella pneumoniaeandEscherichia coli. Correlating these experimental data via an AI‐derived relationship, IDentif.AI rapidly determines a ranked list of drug combinations in the search space of over half a million possible combinations. Meropenem is found to strongly synergize with low doses of the anticancer drug bleomycin, showing broad‐spectrum, bactericidal activity against nine isolates across three CRE species in rich and minimal media with no synergistic cytotoxicity on mammalian cells. Synergy is also detected between bleomycin and other key carbapenems in clinical use (imipenem, ertapenem). Bleomycin/carbapenem appears to be a promising combination therapy for treating various CRE infections. IDentif.AI shows profound capability of identifying pan‐active drug combinations against a family of bacteria through surveying strains from different species in parallel.