bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of the literature on family therapy with adolescents 1979–1987
Authors: Breunlin Douglas C. , Breunlin Cynthia , Kearns David L. , Russell William P. 
Published: August 2006

SummarySince the initial publication of our article, significant developments have occurred in the literature pertaining to the application of family therapy to problems of adolescents. A primary change has been quantitative. As is evident from the problem listing above, a great number of articles have been written addressing a continually expanding array of presenting complaints.Similarly, the recent review clearly indicated that a full range of family therapy models has been represented in the literature since 1979. In a general sense, the family therapy models described in our original paper—Psychoanalytic, Behavioral, and Systems‐oriented (including Structural, and Strategic family therapy)—have continued to receive attention. It is also clear that family therapists working with adolescents have demonstrated a willingness to experiment with new theoretical developments. Especially noteworthy are the relatively recent applications of Systemic family therapy (Milan model) to problems of adolescents. There is also growing evidence that single model approaches to adolescents may be less desirable than approaches that combine the strengths of several models in an integrated or carefully eclectic fashion.A number of authors have suggested guidlines for planning and conducting family therapy with adolescents. A survey of the various sets of guidelines revealed some of the continuing dilemmas and controversies that exist in the field. The suggestions offered vary according to the authors' theoretical orientations. Of particular interest are guidelines that are organized around such concepts as “stages” or “family typology”. The results reported in the various outcomes studies clearly suggested that family therapy with adolescents is a viable treatment approach, one that in many instances produces results often exceeding those seen when other, more traditional treatments are employed.In the 1979 article, we took the position that family therapy offered “new and exciting directions” for the treatment of adolescent disturbances. We still think this is true. Family therapy, in its various forms, has proven to be a well established approach to the treatment of adolescent problems. Finally, we believe this area will continue through careful consideration of three issues: first, the continued application of new developments in the field therapy to the treatment of problems of adolescents; second, further elaboration of guidelines for therapy that are based on particular treatment models; and third, the design of more carefully constructed outcome studies that evaluate the comparative effectiveness of different family therapy models in dealing with particular presenting problems, family characteristics, and stages of adolescent development.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Authors: Stamatakis Alexandros 
Published: August 2006

Abstract
Summary: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Γ yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets ≥4000 taxa it also runs 2–3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25 057 (1463 bp) and 2182 (51 089 bp) taxa, respectively.
Availability:
Contact: Alexandros.Stamatakis@epfl.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
Dockground resource for studying protein–protein interfaces
Authors: Douguet Dominique , Chen Huei-Chi , Tovchigrechko Andrey , Vakser Ilya A. 
Published: August 2006

Abstract
Motivation: Public resources for studying protein interfaces are necessary for better understanding of molecular recognition and developing intermolecular potentials, search procedures and scoring functions for the prediction of protein complexes.
Results: The first release of the Dockground resource implements a comprehensive database of co-crystallized (bound–bound) protein–protein complexes, providing foundation for the upcoming expansion to unbound (experimental and simulated) protein–protein complexes, modeled protein–protein complexes and systematic sets of docking decoys. The bound–bound part of Dockground is a relational database of annotated structures based on the Biological Unit file (Biounit) provided by the RCSB as a separated file containing probable biological molecule. Dockground is automatically updated to reflect the growth of PDB. It contains 67 220 pairwise complexes that rely on 14 913 Biounit entries from 34 778 PDB entries (January 30, 2006). The database includes a dynamic generation of non-redundant datasets of pairwise complexes based either on the structural similarity (SCOP classification) or on user-defined sequence identity. The growing Dockground resource is designed to become a comprehensive public environment for developing and validating new methodologies for modeling of protein interactions.
Availability: Dockground is available at . The current first release implements the bound–bound part.
Contact: douguet@cbs.cnrs.fr
MMM: a sequence-to-structure alignment protocol
Authors: Rai Brajesh K. , Madrid-Aliste Carlos J. , Fajardo J. Eduardo , Fiser András 
Published: August 2006

Abstract
Motivation: Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models.
Results: Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The alternatively aligned regions from the input alignment set are combined according to their fit in the structural environment of the template structure. The resulting, optimally spliced MMM alignment is used as input to an automated comparative modeling module to produce a full atom model.
Availability: The MMM server is freely accessible at
Contact: andras@fiserlab.org
MARD: a new method to detect differential gene expression in treatment-control time courses
Authors: Cheng Chao , Ma Xiaotu , Yan Xiting , Sun Fengzhu , Li Lei M. 
Published: August 2006

Abstract
Motivation: Characterizing the dynamic regulation of gene expression by time course experiments is becoming more and more important. A common problem is to identify differentially expressed genes between the treatment and control time course. It is often difficult to compare expression patterns of a gene between two time courses for the following reasons: (1) the number of sampling time points may be different or hard to be aligned between the treatment and the control time courses; (2) estimation of the function that describes the expression of a gene in a time course is difficult and error-prone due to the limited number of time points. We propose a novel method to identify the differentially expressed genes between two time courses, which avoids direct comparison of gene expression patterns between the two time courses.
Results: Instead of attempting to ‘align’ and compare the two time courses directly, we first convert the treatment and control time courses into neighborhood systems that reflect the underlying relationships between genes. We then identify the differentially expressed genes by comparing the two gene relationship networks. To verify our method, we apply it to two treatment-control time course datasets. The results are consistent with the previous results and also give some new biologically meaningful findings.
Availability: The algorithm in this paper is coded in C++ and is available from
Contact: lilei@usc.edu; chaochen@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Maximum likelihood of phylogenetic networks
Authors: Jin Guohua , Nakhleh Luay , Snir Sagi , Tuller Tamir 
Published: August 2006

Abstract
Motivation: Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative.
Results: In this article we provide a new HGT-oriented likelihood framework for many problems that involve phylogeny-based HGT detection and reconstruction. Beside the formulation of various likelihood criteria, we show that most of these problems are NP-hard, and offer heuristics for efficient and accurate reconstruction of HGT under these criteria. We implemented our heuristics and used them to analyze biological as well as synthetic data. In both cases, our criteria and heuristics exhibited very good performance with respect to identifying the correct number of HGT events as well as inferring their correct location on the species tree.
Availability: Implementation of the criteria as well as heuristics and hardness proofs are available from the authors upon request. Hardness proofs can also be downloaded at
Contact: tamirtul@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
TESD: a transposable element dynamics simulation environment
Authors: Deceliere Grégory , Letrillard Yann , Charles Sandrine , Biémont Christian 
Published: August 2006

Abstract
Various mathematical models have been used to explore the dynamics of transposable elements (TEs) within their host genomes. However, numerous factors can influence their dynamics, and we know only little about the dynamics of TEs when they first began to invade populations. In addition, the influence of population structuring has only recently been investigated. Transposable Element Simulator Dynamics, a population genomics simulation environment, has therefore been developed to provide a simple tool for analyzing the dynamics of TEs in a community based on (i) various TE parameters, such as the transposition and excision rates, the recombination rate and the coefficient of selection against TE insertions; and (ii) population parameters, such as population size and migration rates. The simulations can be used to illustrate the dynamic fate of TEs in structured populations, can be extended by using more specific molecular or demographic models, and can be useful for teaching population genetics and genomics.
Availability: TESD is distributed under GPL from the Pôle Bioinformatique Lyonnais (PBIL) web server at
Contact: biemont@biomserv.univ-lyon1.fr
Will African Agriculture Survive Climate Change?
Authors: Kurukulasuriya Pradeep , Mendelsohn Robert , Hassan Rashid , Benhin James , Deressa Temesgen , Diop Mbaye , Eid Helmy Mohamed , Fosu K. Yerfi , Gbetibouo Glwadys , Jain Suman , Mahamadou Ali , Mano Renneth , Kabubo-Mariara Jane , El-Marsafawy Samia , Molua Ernest , Ouda Samiha , Ouedraogo Mathieu , Séne Isidor , Maddison David , Seo S. Niggol , Dinar Ariel 
Published: August 2006

Abstract
Measurement of the likely magnitude of the economic impact of climate change on African agriculture has been a challenge. Using data from a survey of more than 9,000 farmers across 11 African countries, a cross-sectional approach estimates how farm net revenues are affected by climate change compared with current mean temperature. Revenues fall with warming for dryland crops (temperature elasticity of −1.9) and livestock (−5.4), whereas revenues rise for irrigated crops (elasticity of 0.5), which are located in relatively cool parts of Africa and are buffered by irrigation from the effects of warming. At first, warming has little net aggregate effect as the gains for irrigated crops offset the losses for dryland crops and livestock. Warming, however, will likely reduce dryland farm income immedia-tely. The final effects will also depend on changes in precipitation, because revenues from all farm types increase with precipitation. Because irrigated farms are less sensitive to climate, where water is available, irrigation is a practical adaptation to climate change in Africa.
Incidence and Risk of Adverse Perioperative Events among Surgical Patients Taking Traditional Chinese Herbal Medicines
Authors: Lee Anna , Chui Po Tong , Aun Cindy S. T. , Lau Angel S. C. , Gin Tony 
Published: August 2006

Background
The use of traditional Chinese herbal medicines (TCHMs) among the presurgical population is widespread, but their impact on perioperative patient care is unclear. The authors estimated the incidence and risk of TCHM-related perioperative events.

Methods
In a Hong Kong cohort study, 601 patients undergoing major elective surgery were asked about their Western medicine and TCHM use in the 2 weeks before surgery. Unanticipated perioperative events were noted by attending anesthesiologists, blinded to patients' use of specific TCHMs. Modified Poisson regression models were used to obtain the relative risk of combined endpoints of perioperative events associated with TCHM use.

Results
Of the 601 patients, 483 patients (80%) took self-prescribed TCHM, and 47 (8%) took TCHM by prescription (with or without self-prescribed TCHM) in the 2 weeks before surgery. The crude incidences of any combined endpoints of preoperative, intraoperative, and postoperative events were 23% (95% confidence interval, 19-26%), 74% (95% confidence interval, 71-78%), and 63% (95% confidence interval, 59-66%), respectively. Compared with nonusers, patients who took TCHM by prescription were more likely to have a preoperative event (adjusted relative risk, 2.21; 95% confidence interval, 1.14-4.29). The authors present four case reports to highlight the effect of TCHM by prescription on prolonged activated partial thromboplastin time and hypokalemia in the preoperative period. In contrast, there was no significant association between the use of any type of TCHM and the occurrence of either intraoperative or postoperative events.

Conclusions
The use of TCHM by prescription near the time of surgery should be discouraged because of the increased risk of adverse events in the preoperative period.
Closed-loop Control of Mean Arterial Blood Pressure during Surgery with Alfentanil
Authors: Luginbühl Martin , Bieniok Christian , Leibundgut Daniel , Wymann Rolf , Gentilini Andrea , Schnider Thomas W. 
Published: August 2006

Background
In contrast to hypnosis, there is no surrogate parameter for analgesia in anesthetized patients. Opioids are titrated to suppress blood pressure response to noxious stimulation. The authors evaluated a novel model predictive controller for closed-loop administration of alfentanil using mean arterial blood pressure and predicted plasma alfentanil concentration (Cp Alf) as input parameters.

Methods
The authors studied 13 healthy patients scheduled to undergo minor lumbar and cervical spine surgery. After induction with propofol, alfentanil, and mivacurium and tracheal intubation, isoflurane was titrated to maintain the Bispectral Index at 55 (+/- 5), and the alfentanil administration was switched from manual to closed-loop control. The controller adjusted the alfentanil infusion rate to maintain the mean arterial blood pressure near the set-point (70 mmHg) while minimizing the Cp Alf toward the set-point plasma alfentanil concentration (Cp Alfref) (100 ng/ml).

Results
Two patients were excluded because of loss of arterial pressure signal and protocol violation. The alfentanil infusion was closed-loop controlled for a mean (SD) of 98.9 (1.5)% of presurgery time and 95.5 (4.3)% of surgery time. The mean (SD) end-tidal isoflurane concentrations were 0.78 (0.1) and 0.86 (0.1) vol%, the Cp Alf values were 122 (35) and 181 (58) ng/ml, and the Bispectral Index values were 51 (9) and 52 (4) before surgery and during surgery, respectively. The mean (SD) absolute deviations of mean arterial blood pressure were 7.6 (2.6) and 10.0 (4.2) mmHg (P = 0.262), and the median performance error, median absolute performance error, and wobble were 4.2 (6.2) and 8.8 (9.4)% (P = 0.002), 7.9 (3.8) and 11.8 (6.3)% (P = 0.129), and 14.5 (8.4) and 5.7 (1.2)% (P = 0.002) before surgery and during surgery, respectively. A post hoc simulation showed that the Cp Alfref decreased the predicted Cp Alf compared with mean arterial blood pressure alone.

Conclusion
The authors' controller has a similar set-point precision as previous hypnotic controllers and provides adequate alfentanil dosing during surgery. It may help to standardize opioid dosing in research and may be a further step toward a multiple input-multiple output controller.
Airway Injuries after One-lung Ventilation: A Comparison between Double-lumen Tube and Endobronchial Blocker
Authors: Knoll Heike , Ziegeler Stephan , Schreiber Jan-Uwe , Buchinger Heiko , Bialas Patric , Semyonov Kirill , Graeter Thomas , Mencke Thomas 
Published: August 2006

Background
Vocal cord injuries, postoperative hoarseness, and sore throat are common complications after general anesthesia. One-lung ventilation can be achieved via two techniques: double-lumen endotracheal tube or endobronchial blocker such as the Arndt blocker. The current study was designed to assess the impact of these techniques for one-lung ventilation on the incidence and severity of postoperative hoarseness, vocal cord lesions, and sore throat.

Methods
In this prospective trial, 60 patients were randomly assigned to two groups. One-lung ventilation was achieved with either an endobronchial blocker (blocker group) or a double-lumen-tube (double-lumen group). Postoperative hoarseness and sore throat were assessed at 24, 48, and 72 h after surgery. Bronchial injuries and vocal cord lesions were examined by bronchoscopy immediately after surgery.

Results
In 56 included patients, postoperative hoarseness occurred significantly more frequently in the double-lumen group compared with the blocker group: 44% versus 17%, respectively (P = 0.046). Similar findings were observed for vocal cord lesions: 44% versus 17%, respectively (P = 0.046). The incidence of bronchial injuries was comparable between groups (P = 0.540). Cumulative number of days with hoarseness and sore throat were significantly increased in the double-lumen group compared with the blocker group (P < 0.01). No major complications such as bronchial ruptures were observed.

Conclusions
Clinicians should be aware of an increased incidence of minor airway injuries that may impair patient satisfaction when using a double-lumen tube instead of an endobronchial blocker for one-lung ventilation.
Human Skin Microcirculation after Brachial Plexus Block Evaluated by Wavelet Transform of the Laser Doppler Flowmetry Signal
Authors: Landsverk Svein A. , Kvandal Per , Kjelstrup Trygve , Benko Uros , Bernjak Alan , Stefanovska Aneta , Kvernmo Hebe , Kirkeboen Knut A. 
Published: August 2006

Background
The skin microcirculation may be evaluated noninvasively by laser Doppler flowmetry and iontophoresis with acetylcholine and sodium nitroprusside. Wavelet transform of the perfusion signal shows periodic oscillations of five characteristic frequencies in the interval 0.0095-1.6 Hz. The aim of the current study was to investigate alterations in skin microcirculation induced by brachial plexus block, with emphasis on the periodic oscillations.

Methods
Healthy nonsmokers undergoing hand surgery (n = 13) were anesthetized with brachial plexus block, using bupivacaine, lidocaine, and epinephrine. Skin microcirculation was evaluated by laser Doppler flowmetry and iontophoresis with acetylcholine and sodium nitroprusside before and after brachial plexus block. Wavelet transform of the perfusion signal was performed. As a control group, 10 healthy nonsmokers were included.

Results
In the anesthetized arm, skin perfusion after brachial plexus block increased from 19 (12-30) to 24 (14-39) arbitrary units (P < 0.01). A significant increase was also seen in the contralateral arm from 17 (14-32) to 20 (14-42) arbitrary units (P < 0.01). After brachial plexus block, spectral analysis revealed a significant reduction in relative amplitude of the oscillatory components within the 0.0095- to 0.021- (P < 0.001) and 0.021- to 0.052-Hz (P < 0.001) intervals in the anesthetized arm.

Conclusion
Alterations in skin microcirculation induced by brachial plexus block can be evaluated by wavelet transform of the laser Doppler flowmetry signal. Brachial plexus block reduces the oscillatory components within the 0.0095- to 0.021- and 0.021- to 0.052-Hz intervals of the perfusion signal. These alterations are related to inhibition of sympathetic activity and a possible impairment of endothelial function.
Association between Increases in Urinary Neutrophil Gelatinase–associated Lipocalin and Acute Renal Dysfunction after Adult Cardiac Surgery
Authors: Wagener Gebhard , Jan Michael , Kim Mihwa , Mori Kiyoshi , Barasch Jonathan M. , Sladen Robert N. , Lee H Thomas 
Published: August 2006

Background
Acute renal dysfunction (ARD) and subsequent acute renal failure after cardiac surgery are associated with high mortality and morbidity. Early therapeutic or preventive intervention is hampered by the lack of an early biomarker for acute renal injury. Recent studies showed that urinary neutrophil gelatinase-associated lipocalin (NGAL or lipocalin 2) is up-regulated early (within 1-3 h) after murine renal injury and in pediatric ARD after cardiac surgery. The authors hypothesized that postoperative urinary NGAL concentrations are increased in adult patients developing ARD after cardiac surgery compared with patients without ARD.

Methods
After institutional review board approval, 81 cardiac surgical patients were prospectively studied. Urine samples were collected immediately before incision and at various time intervals after surgery for NGAL analysis by quantitative immunoblotting. ARD was defined as peak postoperative serum creatinine increase by 50% or greater compared with preoperative serum creatinine.

Results
Sixteen of 81 patients (20%) developed postoperative ARD, and the mean urinary NGAL concentrations in patients who developed ARD were significantly higher early after surgery (after 1 h: 4,195 +/- 6,520 [mean +/- SD] vs. 1,068 +/- 2,129 ng/ml; P < 0.01) compared with patients who did not develop ARD. Mean urinary NGAL concentrations continued to increase and remained significantly higher at 3 and 18 h after cardiac surgery in patients with ARD. In contrast, urinary NGAL in patients without ARD decreased rapidly after cardiac surgery.

Conclusions
Patients developing postoperative ARD had significantly higher urinary NGAL concentrations early after cardiac surgery. Urinary NGAL may therefore be a useful early biomarker of ARD after cardiac surgery. These findings may facilitate the early detection of acute renal injury and potentially prevent progression to acute renal failure.