bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pressure Ulcer Prevalence in Long‐Term Nursing Home Residents Since the Implementation of OBRA '87
Authors: Coleman Eric A. , Martau James M. , Lin Michael K. , Kramer Andrew M. 
Published: July 2002

OBJECTIVES: To evaluate change in pressure ulcer prevalence in long‐term nursing home residents since the implementation of the Omnibus Budget Reconciliation Act of 1987 (OBRA '87).DESIGN: Cross‐sectional comparison of two time periods.SETTING: Ninety‐two nursing homes scheduled for a quality‐of‐care survey randomly selected from 22 representative states.PARTICIPANTS: Four thousand six hundred seventy‐nine residents who had resided in the facility for at least 100 days were evaluated: 2,336 during 1992–1994 and 2,343 during 1997–1998.MEASUREMENTS: Trained registered nurses collected data on pressure ulcer prevalence, stage, and risk factors from medical record review during on‐site evaluations. Risk‐adjusted differences were estimated using logistic regression.RESULTS: Unadjusted prevalence rates for all stages of pressure ulcers (8.52% vs 8.54%, P = .983) and those rated stage 2 or greater (5.31% vs 5.63%, P = .624) did not differ between the two time periods. After adjustment for urinary incontinence, immobility, poor nutrition, and history of previous pressure ulcers, the relative odds of having a pressure ulcer in 1992/4 versus 1997/8 was 1.06 (95% confidence interval (CI) = 0.84–1.34) for all stages and 1.21 (95% CI = 0.92–1.60) for stages 2 and greater.CONCLUSIONS: No change in pressure ulcer prevalence was demonstrated since implementation of OBRA '87 in this nationally derived sample of long‐term nursing home residents.
CARS spectroscopy of O2(1Δg) from the Hartley band photodissociation of O3: Dynamics of the dissociation
Authors: Valentini James J. , Gerrity Daniel P. , Phillips David L. , Nieh Jong-Chen , Tabor Kevin D. 
Published: July 2002

Rotationally and vibrationally resolved CARS spectra of the O2(1Δg) photofragment produced by the photodissociation of O3 at 17 wavelengths between 230 and 311 nm are reported. The spectra are taken under collision-free conditions, therefore, they reveal the nascent rotational and vibrational state distributions of the O2(1Δg) photofragment. At all photolysis wavelengths studied the vibrational distribution peaks very sharply at v=0, although all energetically allowed vibrational states are observed. The rotational state distributions are narrow, and peak typically at high J. The rotational distribution shifts to lower J as the photolysis wavelength increases. These observations imply vibrationally adiabatic, rotationally impulsive energy release in the dissociation. The shape and width of the rotational distributions can be completely accounted for by the spread in the O3 thermal rotation and zero-point vibration contributions to the O2(1Δg) photofragment angular momentum. The most striking observation about the O2(1Δg) photofragment quantum state distribution is an apparent propensity for even-J states. Experiments with 18O enriched ozone indicate that this propensity is observed only for 16O16O, not for 18O16O, and by implication not for 17O16O. We show that this is the consequence of a selective depletion of only odd-J rotational states of 16O16O(1Δg) by a curve crossing to O2(3Σg), but an equal depletion of both even-J and odd-J rotational states of 18O16O and 17O16O(1Δg) by the curve crossing. The odd-J selectivity for 16O16O is a consequence of the restriction of 3Σg to only odd-J states, due to the requirement of even nuclear exchange symmetry for this homonuclear species with spin-zero nuclei. As a result of the different curve crossing behavior, the quantum yield for 3Σg is twice as great for 18O16O and 17O16O as it is for 16O16O, and this imposes a mass-independent
isotopic fractionation in the photodissociation: the O2(1Δg) fragments are depleted of 17O and 18O, while the O2(3Σg) fragments are enriched in these isotopes.
Analysis of C-cadherin Regulation during Tissue Morphogenesis with an Activating Antibody
Authors: Zhong Yun , Brieher William M. , Gumbiner Barry M. 
Published: July 2002

The regulation of cadherin-mediated adhesion at the cell surface underlies several morphogenetic processes. To investigate the role of cadherin regulation in morphogenesis and to begin to analyze the molecular mechanisms of cadherin regulation, we have screened for monoclonal antibodies (mAbs) that allow us to manipulate the adhesive state of the cadherin molecule.
Xenopus C-cadherin is regulated during convergent extension movements of gastrulation. Treatment of animal pole tissue explants (animal caps) with the mesoderm-inducing factor activin induces tissue elongation and decreases the strength of C-cadherin–mediated adhesion between blastomeres (Brieher, W.M., and B.M. Gumbiner. 1994. J. Cell Biol. 126:519–527). We have generated a mAb to C-cadherin, AA5, that restores strong adhesion to activin-treated blastomeres. This C-cadherin activating antibody strongly inhibits the elongation of animal caps in response to activin without affecting mesodermal gene expression. Thus, the activin-induced decrease in C-cadherin adhesive activity appears to be required for animal cap elongation.
Regulation of C-cadherin and its activation by mAb AA5 involve changes in the state of C-cadherin that encompass more than changes in its homophilic binding site. Although mAb AA5 elicited a small enhancement in the functional activity of the soluble C-cadherin ectodomain (CEC1-5), it was not able to restore cell adhesion activity to mutant C-cadherin lacking its cytoplasmic tail. Furthermore, activin treatment regulates the adhesion of Xenopus blastomeres to surfaces coated with two other anti–C-cadherin mAbs, even though these antibodies probably do not mediate adhesion through a normal homophilic binding mechanism. Moreover, mAb AA5 restores strong adhesion to these antibodies. mAb AA5 only activates adhesion of blastomeres to immobilized CEC1-5 when it binds to C-cadherin on the cell surface. It does not work when added to CEC1-5 on the substrate. Together these findings suggest that the regulation of C-cadherin by activin and its activation by mAb AA5 involve changes in its cellular organization or interactions with other cell components that are not intrinsic to the isolated protein.
The BioCatalog.
Authors: Rodriguez-Tom√© P 
Published: July 2002

Abstract
MOTIVATION: The BioCatalog is a database of information on software of interest in molecular biology and genetics. The programs are grouped by domain of interest. AVAILABILITY: The BioCatalog is freely distributed as ASCII files. It can be searched through its Web interface at http://www.ebi.ac.uk/biocat. CONTACT: biocat@ebi. ac.uk
The bio-objects project. Part I: the object data model core elements.
Authors: Maltchenko S Z 
Published: July 2002

Abstract
MOTIVATION: Scientific data reside in a number of different data sources, both public and commercial, and are accessible through various software applications. Data and software interoperability is becoming a critical issue in the research community. In our opinion, the need to develop a unified object model for biotechnology must be recognized. Herein, we present a prototype and core elements for the Object Data Model, a central part of our future commercial product development. RESULTS: We have designed a first layer of the Object Data Model that will be used for further commercial application development. The CBioBase object was designed as a citable, stable and core data element for the Object Data Model. General relationships between objects and application components were established. AVAILABILITY: Software tools will be provided with a future DNASIS product to access various elements of the Object Model. We are planning to assemble C++ libraries and Java binary files into BioObjects SDK (software development kit) for those interested in software implementation using the described object model. CONTACT: smaltch@msn.com or smaltch@hitachi-soft.com
VIRTLAB: a virtual molecular biology laboratory.
Authors: Iazzetti G , Santini G , Rau M , Bucci E , Calogero R A 
Published: July 2002

Abstract
SUMMARY: VIRTLAB is a self-training program based on PBL (Problem-Based-Learning Pathway) built to simulate a molecular biology laboratory. It has been designed to stimulate students in the biological sciences to analyse and solve molecular biology problems using standard laboratory techniques (e.g. restriction enzyme digestions, analytical and preparative agarose gels, DNA cloning and sequencing, etc.) and can thus be viewed as a teaching aid. AVAILABILITY: The VIRTLAB package is distributed free of charge to non-profit organisations by the authors (virtlab@biol.dgbm. unina.it). On-line help and tutorials, available now in English, French, Italian, and shortly in German, are provided with the software or at http://biol.dgbm.unina.it:8080/virtlab.html++ +
The domain-server: direct prediction of protein domain-homologies from BLAST search.
Authors: Murvai J , Vlahovicek K , Barta E , Parthasarathy S , Hegyi H , Pfeiffer F , Pongor S 
Published: July 2002

Abstract
RESULTS: A WWW server for protein domain homology prediction, based on BLAST search and a simple data-mining algorithm (Hegyi,H. and Pongor,S. (1993) Comput. Appl. Biosci., 9, 371-372), was constructed providing a tabulated list and a graphic plot of similarities. AVAILABILITY: http://www.icgeb.trieste.it/domain. Mirror site is available at http://sbase.abc.hu/domain. A standalone programme will be available on request. SUPPLEMENTARY INFORMATION: A series of help files is available at the above addresses.
Wavelet change-point prediction of transmembrane proteins
Authors: Lio Pietro , Vannucci Marina 
Published: July 2002

Abstract
Motivation: A non-parametric method, based on a wavelet data-dependent threshold technique for change-point analysis, is applied to predict location and topology of helices in transmembrane proteins. A new propensity scale generated from a transmembrane helix database is proposed.
Results: We show that wavelet change-point performs well for smoothing hydropathy and transmembrane profiles generated using different scales. We investigate which wavelet bases and threshold functions are overall most appropriate to detect transmembrane segments. Prediction accuracy is based on the analysis of two data sets used as standard benchmarks for transmembrane prediction algorithms. The analysis of a test set of 83 proteins results in accuracy per segment equal to 98.2%; the analysis of a 48 proteins blind-test set, i.e. containing proteins not used to generate the propensity scales, results in accuracy per segment equal to 97.4%. We believe that this method can also be applied to the detection of boundaries of other patterns such as G + Cisochores and dot-plots.
Availability: The transmembrane database, TMALN and source code are available upon request from the authors.
Contact: plio@hgmp.mrc.ac.uk
Polylink: to support two-point linkage analysis in
autotetraploids
Authors: He Yang , Xu Xiangming , Tobutt Kenneth R. , Ridout Martin S. 
Published: July 2002

Abstract
Summary: Polylink runs under Microsoft Windows (95 or later). It performs various calculations that are useful for investigating two-point linkage analysis for autopolyploids, based on the random chromosome pairing model. These include calculation of offspring phenotypic probabilities as functions of the recombination fraction, \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(r\) \end{document}calculation of theoretical standard errors for the maximum likelihood estimator of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(r\) \end{document}and numerical computation of maximum likelihood estimates. It also includes simulation facilities.
Availability: Polylink is free and available from Xiangming Xu via email
Contact: xiangming.xu@hri.ac.uk
* To whom correspondence should be addressed.
Role of the single cysteine residue, Cys 3, of human and bovine cystatin B (stefin B) in the inhibition of cysteine proteinases
Authors: Pol Ewa , Björk Ingemar 
Published: July 2002

AbstractCystatin B is unique among cysteine proteinase inhibitors of the cystatin superfamily in having a free Cys in the N‐terminal segment of the proteinase binding region. The importance of this residue for inhibition of target proteinases was assessed by studies of the affinity and kinetics of interaction of human and bovine wild‐type cystatin B and the Cys 3‐to‐Ser mutants of the inhibitors with papain and cathepsins L, H, and B. The wild‐type forms from the two species had about the same affinity for each proteinase, binding tightly to papain and cathepsin L and more weakly to cathepsins H and B. In general, these affinities were appreciably higher than those reported earlier, perhaps because of irreversible oxidation of Cys 3 in previous work. The Cys‐to‐Ser mutation resulted in weaker binding of cystatin B to all four proteinases examined, the effect varying with both the proteinase and the species variant of the inhibitor. The affinities of the human inhibitor for papain and cathepsin H were decreased by threefold to fourfold and that for cathepsin B by ∼20‐fold, whereas the reductions in the affinities of the bovine inhibitor for papain and cathepsins H and B were ∼14‐fold, ∼10‐fold and ∼300‐fold, respectively. The decreases in affinity for cathepsin L could not be properly quantified but were greater than threefold. Increased dissociation rate constants were responsible for the weaker binding of both mutants to papain. By contrast, the reduced affinities for cathepsins H and B were due to decreased association rate constants. Cys 3 of both human and bovine cystatin B is thus of appreciable importance for inhibition of cysteine proteinases, in particular cathepsin B.
NMR of hydrogen bonding in cold‐shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths
Authors: Alexandrescu Andrei T. , Snyder Doug R. , Abildgaard Frits 
Published: July 2002

AbstractHydrogen bonding in cold‐shock protein A of Escherichia coli has been investigated using long‐range HNCO spectroscopy. Nearly half of the amide protons involved in hydrogen bonds in solution show no measurable protection from exchange in water, cautioning against a direct correspondence between hydrogen bonding and hydrogen exchange protection. The N to O atom distance across a hydrogen bond, RNO, is related to the size of the 3hJNC' trans hydrogen bond coupling constant and the amide proton chemical shift. Both NMR parameters show poorer agreement with the 2.0‐Å resolution X‐ray structure of the cold‐shock protein studied by NMR than with a 1.2‐Å resolution X‐ray structure of a homologous cold‐shock protein from the thermophile B. caldolyticus. The influence of crystallographic resolution on comparisons of hydrogen bond lengths was further investigated using a database of 33 X‐ray structures of ribonuclease A. For highly similar structures, both hydrogen bond RNO distance and Cα coordinate root mean square deviations (RMSD) show systematic increases as the resolution of the X‐ray structure used for comparison decreases. As structures diverge, the effects of coordinate errors on RNO distance and Cα coordinate root mean square deviations become progressively smaller. The results of this study are discussed with regard to the influence of data precision on establishing structure similarity relationships between proteins.
Changes in Performance Measures and Service Volume at US Federally Qualified Health Centers During the COVID-19 Pandemic
Authors: Cole Megan B. , Lee Eun Kyung , Frogner Bianca K. , Wright Brad 
Published: April 2023

ImportanceStay-at-home orders, site closures, staffing shortages, and competing COVID-19 testing and treatment needs all potentially decreased primary care access and quality during the COVID-19 pandemic. These challenges may have especially affected federally qualified health centers (FQHCs), which serve patients with low income nationwide.ObjectiveTo examine changes in FQHCs’ quality-of-care measures and visit volumes in 2020 to 2021 vs prepandemic.Design, Setting, and ParticipantsThis cohort study used a census of US FQHCs to calculate changes in outcomes between 2016 and 2021 using generalized estimating equations.Main Outcomes and MeasuresTwelve quality-of-care measures and 41 visit types based on diagnoses and services rendered, measured at the FQHC-year level.ResultsA total of 1037 FQHCs were included, representing 26.6 million patients (63% 18-64 years old; 56% female) in 2021. Despite upward trajectories for most measures prepandemic, the percentage of patients served by FQHCs receiving recommended care or achieving recommended clinical thresholds showed a statistically significant decrease between 2019 and 2020 for 10 of 12 quality measures. For example, declines were observed for cervical cancer screening (−3.8 percentage points [pp]; 95% CI, −4.3 to −3.2 pp), depression screening (−7.0 pp; 95% CI, −8.0 to −5.9 pp), and blood pressure control in patients with hypertension (−6.5 pp; 95% CI, −7.0 to −6.0 pp). By 2021, only 1 of these 10 measures returned to 2019 levels. From 2019 to 2020, 28 of 41 visit types showed a statistically significant decrease, including immunizations (incidence rate ratio [IRR], 0.76; 95% CI, 0.73-0.78), oral examinations (IRR, 0.61; 95% CI, 0.59-0.63), and supervision of infant or child health (IRR, 0.87; 95% CI, 0.85-0.89); 11 of these 28 visits approximated or exceeded prepandemic rates by 2021, while 17 remained below prepandemic rates. Five visit types increased in 2020, including substance use disorder (IRR, 1.07; 95% CI, 1.02-1.11), depression (IRR, 1.06; 95% CI, 1.03-1.09), and anxiety (IRR, 1.16; 95% CI, 1.14-1.19); all 5 continued to increase in 2021.Conclusions and RelevanceIn this cohort study of US FQHCs, nearly all quality measures declined during the first year of the COVID-19 pandemic, with most declines persisting through 2021. Similarly, most visit types declined in 2020; 60% of these remained below prepandemic levels in 2021. By contrast, mental health and substance use visits increased in both years. The pandemic led to forgone care and likely exacerbated behavioral health needs. As such, FQHCs need sustained federal funding to expand service capacity, staffing, and patient outreach. Quality reporting and value-based care models must also adapt to the pandemic’s influence on quality measures.
Suicide Around the Anniversary of a Parent’s Death in Sweden
Authors: Grotta Alessandra , Liu Can , Hiyoshi Ayako , Berg Lisa , Kawachi Ichiro , Saarela Jan , Rostila Mikael 
Published: April 2023

ImportanceBereavement following parental death experienced in adulthood may be associated with suicide over many years, but this risk has received scant attention.ObjectiveTo investigate whether the risk of suicide increases among adult children around the anniversary of a parent’s death.Design, Setting, and ParticipantsThis case-crossover study used Swedish register-based longitudinal data from 1990 to 2016, based on the entire national population. Participants included all adults aged 18 to 65 years who experienced parental death and subsequently died by suicide. Conditional logistic regression was used to quantify the association between the anniversary (or preanniversary and postanniversary periods) and suicide, controlling for time-invariant confounding. All analyses were stratified by sex of the offspring. The analyses were also stratified by the sex of the deceased parent, time since parental death, age, and marital status. Data analyses were performed in June 2022.ExposuresAnniversary of a parent’s death (or preanniversary and postanniversary periods).Main Outcomes and MeasuresSuicide.ResultsOf 7694 individuals who died by suicide (76% intentional self-harm), 2255 (29%) were women, and the median (IQR) age at suicide was 55 (47-62) years. There was evidence of an anniversary reaction among women, with a 67% increase in the odds of suicide when exposed to the period from the anniversary to 2 days after the anniversary, compared with when not being exposed (odds ratio [OR], 1.67; 95% CI, 1.07-2.62). The risk was particularly pronounced among maternally bereaved women (OR, 2.29; 95% CI, 1.20-4.40) and women who were never married (OR, 2.08; 95% CI, 0.99-4.37), although the latter was not statistically significant. An increased risk of suicide from the day before up to the anniversary was observed among women bereaved between the ages of 18 and 34 years (OR, 3.46; 95% CI, 1.14-10.56) and between the ages of 50 and 65 years (OR, 2.53; 95% CI, 1.04-6.15). Men had an attenuated suicide risk for the period from the day before up to the anniversary (OR, 0.57; 95% CI, 0.36-0.92).Conclusions and RelevanceThese findings suggest that the anniversary of a parent’s death is associated with an increased suicide risk among women. Women bereaved at younger or older ages, those who were maternally bereaved, and those who never married appeared to be particularly vulnerable. Families and social and health care professionals need to consider anniversary reactions in suicide prevention.
Incidence and Risk Factors for Eosinophilia and Lung Disease in Biologic‐Exposed Children With Systemic Juvenile Idiopathic Arthritis
Authors: Wobma Holly , Arvila Sage R. , Taylor Maria L. , Lam Ki Pui , Ohashi Marina , Gebhart Catherine , Powers Helene , Case Siobhan , Chandler Mia T. , Chang Margaret H. , Cohen Ezra , Day‐Lewis Megan , Fishman Martha P. , Halyabar Olha , Hausmann Jonathan S. , Hazen Melissa M. , Lee Pui Y. , Lo Mindy S. , Meidan Esra , Roberts Jordan E. , Son Mary Beth F. , Sundel Robert P. , Dedeoğlu Fatma , Nigrovic Peter A. , Casey Alicia , Chang Joyce , Henderson Lauren A. 
Published: April 2023

ObjectiveAlthough interleukin‐1 (IL‐1)/IL‐6 inhibitors are effective therapies for systemic juvenile idiopathic arthritis (JIA), some patients develop eosinophilia and lung disease during treatment. This study was undertaken to retrospectively evaluate incidence and risk factors for eosinophilia and describe lung disease outcomes in IL‐1/IL‐6 inhibitor–exposed patients with systemic JIA.MethodsAmong JIA patients at our institution exposed to interleukin‐1 (IL‐1)/IL‐6 inhibitors (1995–2022), we compared incidence rate of eosinophilia in systemic JIA compared to other JIA, stratified by medication class (IL‐1/IL‐6 inhibitors, other cytokine inhibitors, methotrexate). We used Cox models to identify predictors of eosinophilia during IL‐1/IL‐6 inhibitor use and summarized treatment changes and outcomes after eosinophilia, including lung disease. HLA typing was performed on a clinical or research basis.ResultsThere were 264 new medication exposures in 75 patients with systemic JIA and 41 patients with other JIA. A total of 49% of patients with systemic JIA with HLA typing (n = 45) were positive for HLA–DRB1*15 alleles. Eosinophilia was common during IL‐1/IL‐6 inhibitor use and did not differ by systemic JIA compared to other JIA (0.08 and 0.07 per person‐year, respectively; P = 0.30). Among systemic JIA patients, pretreatment macrophage activation syndrome (MAS) was associated with a higher rate of subsequent eosinophilia on biologic therapy (unadjusted hazard ratio 3.2 [95% confidence interval 1.2–8.3]). A total of 4 of 5 patients who switched therapy within 10 weeks of eosinophilia experienced disease flare compared to none of the patients who continued the original therapy. A total of 8 of 25 patients with pulmonary evaluations had lung disease, and all had severe manifestations of systemic JIA (MAS, intensive care unit stay). One death was attributed to systemic JIA–lung disease.ConclusionEosinophilia is common in JIA patients using IL‐1/IL‐6 inhibitors. Severe disease may be associated with eosinophilia and lung disease in systemic JIA.