Physiotherapists' perspectives of barriers and facilitators to effective community provision after hip fracture: a qualitative study in England.

PURPOSE: to investigate physiotherapists' perspectives of effective community provision following hip fracture. METHODS: qualitative semi-structured interviews were conducted with 17 community physiotherapists across England. Thematic analysis drawing on the Theoretical Domains Framework identified barriers and facilitators to implementation of effective provision. Interviews were complemented by process mapping community provision in one London borough, to identify points of care where suggested interventions are in place and/or could be implemented. RESULTS: four themes were identified: ineffective coordination of care systems, ineffective patient stratification, insufficient staff recruitment and retention approaches and inhibitory fear avoidance behaviours. To enhance care coordination, participants suggested improving access to social services and occupational therapists, maximising multidisciplinary communication through online notation, extended physiotherapy roles, orthopaedic-specific roles and seven-day working. Participants advised the importance of stratifying patients on receipt of referrals, at assessment and into appropriately matched interventions. To mitigate insufficient staff recruitment and retention, participants proposed return-to-practice streams, apprenticeship schemes, university engagement, combined acute-community rotations and improving job description advertisements. To reduce effects of fear avoidance behaviour on rehabilitation, participants proposed the use of patient-specific goals, patient and carer education, staff education in psychological strategies or community psychologist access. Process mapping of one London borough identified points of care where suggested interventions to overcome barriers were in place and/or could be implemented. CONCLUSION: physiotherapists propose that effective provision of community physiotherapy following hip fracture could be improved by refining care coordination, utilising stratification techniques, employing enhanced recruitment and retainment strategies and addressing fear avoidance behaviours.

Lanthanide Contraction in LnF3 (Ln = Ce-Lu) and Its Chemical and Structural Consequences: Part 1: Location of YF3 in the LnF3 Series According to Its Chemical and Structural Characteristics.

A lanthanide contraction(LC) of 14 lanthanides (Ln) from 58Ce to 71Lu consists of the interaction of Ln nucleus with 4f-electrons. Rare earth elements (REEs-R) include Sc, Y, La, and 14 Ln. They are located in 4-6th periods of the subgroup of group III. The electronic structure divides R into short (d- Sc, Y, La) and long (14 f-elements Ce-Lu) homologous series. The most important chemical consequence of LC is the creation of a new conglomerate of 16 RF3 by mixing fluorides of d- (Y, La) and f-elements. This determines the location of YF3 among LnF3. The location of YF3 depends on the structural (formula volumes-Vform) and thermochemical (temperatures and heats of phase transformations, phase diagrams) properties. The location of YF3 between HoF3 and ErF3 was determined by Vform at a standard pressure (Pst) and temperature (Tst). The location of YF3 according to heats of phase transformations ΔHfus and ΔHtrans is in a dimorphic structural subgroup (SSGr) D (Ln = Er-Lu), but without the exact "pseudo ZY". According to the temperatures of phase transformations (Ttrans) in LnF3 (Ln = Dy-Lu), YF3 is located in the SSGr D between ErF3 and TmF3. The ErF3-YF3 and YF3-TmF3 phase diagrams show it to be between ErF3 and TmF3. The crystals of five ß-LnF3 (Ln = Ho-Lu) and ß-YF3 were obtained in identical conditions and their crystal structures were studied. Vform (at Pst and Tst) with "pseudo" atomic numberZY = 67.42 was calculated from the unit cell parameters, which were defined with ±5 × 10-4 Å accuracy. It determines the location of YF3 between HoF3 and ErF3.

Lanthanide Contraction in LnF3 (Ln = Ce-Lu) and Its Chemical and Structural Consequences: Part 2: Specialized Empirical System of R3+ (R = Y, La, and 14 Ln) and F1- Ionic Radii for RF3 Series.

A specialized empirical (Spec-zd Emp) system of ionic radii (SIR) for R = Y3+, La3+, Ln3+, and F1- (R rare earth elements (REE)) was derived from the dependence of lanthanide contraction (LC) on the atomic number (Z) of lanthanides (Ln). LC decreased the radius of the cation with increasing Z. The structures of t-RF3 (LaF3-NdF3, "pseudot-SmF3") of the LaF3 type, 11 ß-LnF3 (Ln = Sm-Lu), and ß-YF3 of the ß-YF3 type were studied. The empirical basis of the shortest (F-F)min and (R-F)min distances was calculated from the structural data for the RF3 complete series. The dependence of (F-F)min on Z reached saturation at Z = 67 (Ho). The base F1- radius r- = 1.2539(16) Å was calculated as the arithmetic mean of five (F-F)min in LnF3 with Ln = Ho-Lu. For the LnF3 series with Ln contributions up to 75 % wt., the dependence of (Ln-F)min on Z reflected the non-uniformity of the 4f orbital filling. SIR was calculated as the difference in the empirical constants of RF3 (ionic radii of (R,Ln)3+ (r+) and F1- (r-)), the change in which was continuous over the series and did not depend on the type of structure: r+ = (ZR-F)min - ½(F-F)min (Z = 57-71). The changes in LC in the LnF3 series were described by a third-degree polynomial. LC reduced r+ by 24% (percentage relative to less) from 1.1671(16) Å (La3+) to 0.9439(17) Å (Lu3+). In the Spec-zd Emp SIR, r+ were constants that did not require corrections for a coordination number (CN). A comparison of r+ in the Spec-zd Emp SIR with other SIRs was performed.

Thermodynamic Origin of Negative Thermal Expansion Based on a Phase Transition-Type Mechanism in the GdF3-TbF3 System.

Multicomponent fluorides of rare earth elements (REEs-R) are phase transition-type negative thermal expansion (NTE-II) materials. NTE-II occurs in RF3-R'F3 systems formed by "mother" single-component dimorphic RF3 (R = Pm, Sm, Eu, and Gd) with a giant NTE-II. There are two structural types of RF3 polymorphic modifications: low-temperature ß-YF3 (ß-) and high-temperature LaF3 (t-). The change in a structural type is accompanied by a density anomaly: a volume of one formula unit (Vform) Vß- >Vt-. The empirical signs of volumetric changes ΔV/V of NTE-II materials were considered. For the GdF3-TbF3 model system, an "operating-temperature window ΔT" and a two-phase composition of NTE-II materials follows from the thermodynamics of chemical systems: the phase rule and the principle of continuity. A necessary and sufficient sign of NTE-II is a combination of polymorphism and the density anomaly. Isomorphism in RF3-R'F3 systems modifies RF3 chemically by forming two-component t- and ß- type R1-xR'xF3solid solutions (ss). Between the two monovariant curves of ss decay, a two-phase area with ΔTtrans > 0 (the "window ΔT") forms. A two-phase composite (t-ss + ß-ss) is an NTE-II material. Its constituent t-ss and ß-ss phases have different Vform corresponding to the selected T. According to the lever rule on a conode, Vform is calculated from the t-ss and ß-ss compositions, which vary with T along two monovariant curves of ss decay. For the GdF3-TbF3 system, ΔV/V = f(T), ΔV/V = f(ΔT) and the "window ΔT" = f(x) dependencies were calculated.

Two-Component Rare-Earth Fluoride Materials with Negative Thermal Expansion Based on a Phase Transition-Type Mechanism in 50 RF3-R'F3 (R = La-Lu) Systems.

The formation of materials with negative thermal expansion (NTE) based on a phase transition-type mechanism (NTE-II) in 50 T-x (temperature-composition) RF3-R'F3 (R = La-Lu) systems out of 105 possible is predicted. The components of these systems are "mother" RF3 compounds (R = Pm, Sm, Eu, and Gd) with polymorphic transformations (PolTrs), which occur during heating between the main structural types of RF3: ß-(ß-YF3) → t-(mineral tysonite LaF3). The PolTr is characterized by a density anomaly: the formula volume (Vform) of the low-temperature modification (Vß-) is higher than that of the high-temperature modification (Vt-) by a giant value (up to 4.7%). In RF3-R'F3 systems, isomorphic substitutions chemically modify RF3 by forming R1-xR'xF3solid solutions (ss) based on both modifications. A two-phase composite (ß-ss + t-ss) is a two-component NTE-II material with adjustable parameters. The prospects of using the material are estimated using the parameter of the average volume change (ΔV/Vav). The Vav at a fixed gross composition of a system is determined by the ß-ss and t-ss decay (synthesis) curves and the temperature T. The regulation of ΔV/Vav is achieved by changing T within a "window ΔT". The available ΔT values are determined using phase diagrams. A chemical classification (ChCl) translates the search for NTE-II materials from 15 RF3 into an array of 105 RF3-R'F3 systems. Phase diagrams are divided into 10 types of systems (TypeSs), in four of which NTE-II materials are formed. The tables of the systems that comprise these TypeSs are presented. The position of Ttrans of the PolTr on the T scale for a short quasi-system (QS) "from PmF3 to TbF3" determines the interval of the ΔTtrans offset achievable in the RF3-R'F3 systems: from -148 to 1186 ± 10 °C. NTE-II fluoride materials exceed known NTE-II materials by almost three times in this parameter. Equilibrium in RF3-R'F3 systems is established quickly. The number of qualitatively different two-component fluoride materials with the giant NTE-II can be increased by more than ten times compared to RF3 with NTE-II.

A systematic, concept-based method of developing the exposure measure for drug safety and effectiveness studies.

PURPOSE: In drug safety and effectiveness studies based on secondary data, the choice of an appropriate exposure measure for a given outcome can be challenging. Different measures of exposure can yield different estimates of treatment effect and safety. There is a knowledge gap with respect to developing and refining measures of drug exposure, to ensure that the exposure measure addresses the study question and is suitable for statistical analysis. METHODS: We present a transparent, step-by-step approach to the development of drug exposure measures involving secondary data. This approach would be of interest to students and investigators with initial training in pharmacoepidemiology. We illustrate the approach using a study about Parkinson's disease. RESULTS: We described the exposure specifications according to the study question. Next, we refined the exposure measure by linking it to knowledge about four major concepts in drug safety and effectiveness studies: drug use patterns, duration, timing, and dose. We then used this knowledge to guide the ultimate choice of exposure measure: time-varying, cumulative 6-month exposure to tamsulosin (a drug used to treat prostate hyperplasia). CONCLUSIONS: The proposed approach links exposure specifications to four major concepts in drug safety and effectiveness studies. Formulating subject-matter knowledge about these major concepts provides an avenue to develop the rationale and specifications for the exposure measure.

Orthopaedic physiotherapists' perceptions of mechanisms for observed variation in the implementation of physiotherapy practices in the early postoperative phase after hip fracture: a UK qualitative study.

OBJECTIVE: to explore physiotherapists' perceptions of mechanisms to explain observed variation in early postoperative practice after hip fracture surgery demonstrated in a national audit. METHODS: a qualitative semi-structured interview study of 21 physiotherapists working on orthopaedic wards at seven hospitals with different durations of physiotherapy during a recent audit. Thematic analysis of interviews drawing on Normalisation Process Theory to aid interpretation of findings. RESULTS: four themes were identified: achieving protocolised and personalised care; patient and carer engagement; multidisciplinary team engagement across the care continuum and strategies for service improvement. Most expressed variation from protocol was legitimate when driven by what is deemed clinically appropriate for a given patient. This tailored approach was deemed essential to optimise patient and carer engagement. Participants reported inconsistent degrees of engagement from the multidisciplinary team attributing this to competing workload priorities, interpreting 'postoperative physiotherapy' as a single professional activity rather than a care delivery approach, plus lack of integration between hospital and community care. All participants recognised changes needed at both structural and process levels to improve their services. CONCLUSION: physiotherapists highlighted an inherent conflict between their intention to deliver protocolised care and allowing for an individual patient-tailored approach. This conflict has implications for how audit results should be interpreted, how future clinical guidelines are written and how physiotherapists are trained. Physiotherapists also described additional factors explaining variation in practice, which may be addressed through increased engagement of the multidisciplinary team and resources for additional staffing and advanced clinical roles.

Variation in surgical demand and time to hip fracture repair: a Canadian database study.

BACKGROUND: Competing demands for operative resources may affect time to hip fracture surgery. We sought to determine the time to hip fracture surgery by variation in demand in Canadian hospitals. METHODS: We obtained discharge abstracts of 151,952 patients aged 65 years or older who underwent surgery for a hip fracture between January, 2004 and December, 2012 in nine Canadian provinces. We compared median time to surgery (in days) when demand could be met within a two-day benchmark and when demand required more days, i.e. clearance time, to provide surgery, overall and stratified by presence of medical reasons for delay. RESULTS: For persons admitted when demand corresponded to a 2-day clearance time, 68% of patients underwent surgery within the 2-day benchmark. When demand corresponded to a clearance time of one week, 51% of patients underwent surgery within 2 days. Compared to demand that could be served within the two-day benchmark, adjusted median time to surgery was 5.1% (95% confidence interval [CI] 4.1-6.1), 12.2% (95% CI 10.3-14.2), and 22.0% (95% CI 17.7-26.2) longer, when demand required 4, 6, and 7 or more days to clear the backlog, respectively. After adjustment, delays in median time to surgery were similar for those with and without medical reasons for delay. CONCLUSION: Increases in demand for operative resources were associated with dose-response increases in the time needed for half of hip fracture patients to undergo surgery. Such delays may be mitigated through better anticipation of day-to-day supply and demand and increased response capability.

Prediction of Protein-ligand Interaction Based on Sequence Similarity and Ligand Structural Features.

Computationally predicting the interaction of proteins and ligands presents three main directions: the search of new target proteins for ligands, the search of new ligands for targets, and predicting the interaction of new proteins and new ligands. We proposed an approach providing the fuzzy classification of protein sequences based on the ligand structural features to analyze the latter most complicated case. We tested our approach on five protein groups, which represented promised targets for drug-like ligands and differed in functional peculiarities. The training sets were built with the original procedure overcoming the data ambiguity. Our study showed the effective prediction of new targets for ligands with an average accuracy of 0.96. The prediction of new ligands for targets displayed the average accuracy 0.95; accuracy estimates were close to our previous results, comparable in accuracy to those of other methods or exceeded them. Using the fuzzy coefficients reflecting the target-to-ligand specificity, we provided predicting interactions for new proteins and new ligands; the obtained accuracy values from 0.89 to 0.99 were acceptable for such a sophisticated task. The protein kinase family case demonstrated the ability to account for subtle features of proteins and ligands required for the specificity of protein-ligand interaction.

Prediction of Protein-Ligand Interaction Based on the Positional Similarity Scores Derived from Amino Acid Sequences.

The affinity of different drug-like ligands to multiple protein targets reflects general chemical-biological interactions. Computational methods estimating such interactions analyze the available information about the structure of the targets, ligands, or both. Prediction of protein-ligand interactions based on pairwise sequence alignment provides reasonable accuracy if the ligands' specificity well coincides with the phylogenic taxonomy of the proteins. Methods using multiple alignment require an accurate match of functionally significant residues. Such conditions may not be met in the case of diverged protein families. To overcome these limitations, we propose an approach based on the analysis of local sequence similarity within the set of analyzed proteins. The positional scores, calculated by sequence fragment comparisons, are used as input data for the Bayesian classifier. Our approach provides a prediction accuracy comparable or exceeding those of other methods. It was demonstrated on the popular Gold Standard test sets, presenting different sequence heterogeneity and varying from the group, including different protein families to the more specific groups. A reasonable prediction accuracy was also found for protein kinases, displaying weak relationships between sequence phylogeny and inhibitor specificity. Thus, our method can be applied to the broad area of protein-ligand interactions.

Spatial features of proteins related to their phosphorylation and associated structural changes.

Protein phosphorylation is widely used in biological regulatory processes. The study of spatial features related to phosphorylation sites is necessary to increase the efficacy of recognition of phosphorylation patterns in protein sequences. Using the data on phosphosites found in amino acid sequences, we mapped these sites onto 3D structures and studied the structural variability of the same sites in different PDB entries related to the same proteins. Solvent accessibility was calculated for the residues known to be phosphorylated. A significant change in accessibility was shown for many sites, but several ones were determined as buried in all the structures considered. Most phosphosites were found in coil regions. However, a significant portion was located in the structurally stable ordered regions. Comparison of structures with the same sites in modified and unmodified states showed that the region surrounding a site could be significantly shifted due to phosphorylation. Comparison between non-modified structures (as well as between the modified ones) suggested that phosphorylation stabilizes one of the possible conformations. The local structure around the site could be changed due to phosphorylation, but often the initial conformation of the site surrounding is not altered within bounds of a rather large substructure. In this case, we can observe an extensive displacement within a protein domain. Phosphorylation without structural alteration seems to provide the interface for domain-domain or protein-protein interactions. Accounting for structural features is important for revealing more specific patterns of phosphorylation. It is also necessary for explaining structural changes as a basis for regulatory processes.

Mammographic non-dense area and breast cancer risk in postmenopausal women: a causal inference approach in a case-control study.

PURPOSE: The association between high mammographic density (MD) and elevated breast cancer risk is well established. However, the role of absolute non-dense area remains unclear. We estimated the effect of the mammographic non-dense area and other density parameters on the risk of breast cancer. METHODS: This study utilizes data from a population-based case-control study conducted in Greater Vancouver, British Columbia, with 477 female postmenopausal breast cancer cases and 588 female postmenopausal controls. MD measures were determined from digitized screening mammograms using computer-assisted software (Cumulus). Marginal odds ratios were estimated by inverse-probability weighting using a causal diagram for confounder selection. Akaike information criteria and receiver operating characteristic curves were used to assess the goodness of fit and predictive power of unconditional logistic models containing MD parameters. RESULTS: The risk of breast cancer is 60% lower for the highest quartile compared to the lowest quartile of mammographic non-dense area (marginal OR 0.40, 95% CI 0.26-0.61, p-trend < 0.001). The cancer risk almost doubles for the highest quartile compared to the lowest quartile of dense area (marginal OR 1.81, 95% CI 1.19-2.43, p-trend < 0.001). For the highest quartile of percent density, breast cancer risk was more than three times higher than for the lowest quartile (marginal OR 3.15, 95% CI 1.90-4.40, p-trend < 0.001). No difference was seen in predictive accuracy between models using percent density alone, dense area alone, or non-dense area plus dense area. CONCLUSIONS: In this study, non-dense area is an independent risk factor after adjustment for dense area and other covariates, inversely related with the risk of breast cancer. However, non-dense area does not improve prediction over that offered by percent density or dense area alone.

Mortality effects of timing alternatives for hip fracture surgery.

BACKGROUND: The appropriate timing of hip fracture surgery remains a matter of debate. We sought to estimate the effect of changes in timing policy and the proportion of deaths attributable to surgical delay. METHODS: We obtained discharge abstracts from the Canadian Institute for Health Information for hip fracture surgery in Canada (excluding Quebec) between 2004 and 2012. We estimated the expected population-average risks of inpatient death within 30 days if patients were surgically treated on day of admission, inpatient day 2, day 3 or after day 3. We weighted observations with the inverse propensity score of surgical timing according to confounders selected from a causal diagram. RESULTS: Of 139 119 medically stable patients with hip fracture who were aged 65 years or older, 32 120 (23.1%) underwent surgery on admission day, 60 505 (43.5%) on inpatient day 2, 29 236 (21.0%) on day 3 and 17 258 (12.4%) after day 3. Cumulative 30-day in-hospital mortality was 4.9% among patients who were surgically treated on admission day, increasing to 6.9% for surgery done after day 3. We projected an additional 10.9 (95% confidence interval [CI] 6.8 to 15.1) deaths per 1000 surgeries if all surgeries were done after inpatient day 3 instead of admission day. The attributable proportion of deaths for delays beyond inpatient day 2 was 16.5% (95% CI 12.0% to 21.0%). INTERPRETATION: Surgery on admission day or the following day was estimated to reduce postoperative mortality among medically stable patients with hip fracture. Hospitals should expedite operating room access for patients whose surgery has already been delayed for nonmedical reasons.

Diagnostic Accuracy of Transient Ischemic Attack from Physician Claims.

BACKGROUND: Hospitalization data underestimate the occurrence of transient ischemic attack (TIA). As TIA is frequently diagnosed in primary care, methodologies for the accurate ascertainment of a TIA from physician claims data are required for surveillance and health systems planning in this population. The present study evaluated the diagnostic accuracy of multiple algorithms for TIA from a longitudinal population-based physician billing database. METHODS: Population-based administrative data from the province of British Columbia were used to identify the base population (1992-2007; N=102,492). Using discharge records for hospital admissions for acute ischemic stroke with a recent (<90 days) TIA as the reference standard, we performed receiver-operating characteristic analyses to calculate sensitivity, specificity, positive and negative predictive values and overall accuracy, and to compare area under the curve for each physician billing algorithm. To evaluate the impact of different case definitions on population-based TIA burden, we also estimated the annual TIA occurrence associated with each algorithm. RESULTS: Physician billing algorithms showed low to moderate sensitivity, with the algorithm for two consecutive physician visits within 90 days showing the highest sensitivity at 37.7% (CI 95%=37.4-38.1). All algorithms demonstrated high specificity and moderate to high overall accuracy, resulting in low positive predictive values (≤5%), low discriminability (0.53-0.57) and high false positive rates (1 - specificity). Population-based estimates of TIA occurrence were comparable to prior studies and declined over time. CONCLUSIONS: Physician billing data have insufficient sensitivity to identify TIAs but may be used in combination with hospital discharge data to improve the accuracy of estimating the population-based occurrence of TIAs.

The burden of second hip fractures: provincial surgical hospitalizations over 15 years.

BACKGROUND: Second hip fractures account for up to 15% of all hip fractures. We sought to determine if the proportion of hip fracture surgeries for second hip fracture changed over time in terms of patient and fracture characteristics. METHODS: We reviewed the records of patients older than 60 years hospitalized for hip fracture surgery between 1990 and 2005 in British Columbia. We studied the proportion of surgeries for second hip fracture among all hip fracture surgeries. Linear regression tested for trends across fiscal years for women and men. RESULTS: We obtained 46 341 patient records. Second hip fracture accounted for 8.3% of hip fracture surgeries. For women the proportion of second hip fracture surgeries increased linearly from 4% to 13% with each age decade (p = 0.001) and across fiscal years (p = 0.002). In men the proportion of second hip fracture surgeries was 5% for each age decade between the ages of 60 and 90 years across fiscal years, increasing to 8% for men older than 90 years across fiscal years (p = 0.20). These sex-specific trends were similar for both pertrochanteric and transcervical fracture types. CONCLUSION: Second hip fracture surgeries account for an increasing proportion of hip fracture surgeries and may require more health care resources to minimize poorer reported outcomes. Future research should determine whether more health care resources are required to manage these patients and optimize their outcomes.

CONTEXTE: Les secondes fractures de la hanche représentent jusqu'à 15 % de la totalité des fractures de la hanche. Nous avons tenté de déterminer si la proportion de chirurgies de seconde fracture de la hanche avait évolué au fil du temps sur le plan des caractéristiques des patients et des fractures. MÉTHODES: Nous avons examiné les dossiers des patients de 60 ans et plus qui avaient été hospitalisés pour une chirurgie de fracture de la hanche entre 1990 et 2005, en Colombie-Britannique. De ce total, nous avons ensuite déterminé le nombre de chirurgies de seconde fracture de la hanche. L'analyse de régression linéaire a déterminé les tendances au cours des années financières pour les femmes et les hommes. RÉSULTATS: Nous avons obtenu 46 341 dossiers de patient. Les secondes fractures de la hanche représentaient 8,3 % de la totalité des chirurgies de fracture de la hanche. Chez les femmes, la proportion de seconde fracture de la hanche augmentait de façon linéaire de 4 % à 13 % pour chaque tranche d'âge de 10 ans (p = 0,001) et sur l'ensemble des années financières (p = 0,002). Chez les hommes, la proportion de chirurgies de seconde fracture de la hanche était de 5 % pour chaque tranche d'âge de 10 ans entre 60 et 90 ans et sur l'ensemble des années financières, et augmentait à 8 % pour les hommes de plus de 90 ans sur l'ensemble des années financières (p = 0,20). Ces tendances selon le sexe étaient similaires tant pour les fractures pertrochantériennes que pour les fractures transcervicales. CONCLUSION: Les chirurgies de seconde fracture de la hanche représentent une proportion croissante de la totalité des chirurgies de fracture de la hanche et pourraient nécessiter davantage de ressources en soins de santé pour minimiser les résultats moins bons signalés. Les recherches futures devraient déterminer s'il faut davantage de ressources de soins de santé pour la prise en charge de ces patients et l'optimisation de leurs résultats.

Prediction of amino acid positions specific for functional groups in a protein family based on local sequence similarity.

The exchange of single amino acid residue in protein can substantially affect the specificity of molecular recognition. Many protein families can be divided into the groups based on specificity to recognized ligands. Prediction of group-discriminating residues within the certain family is extremely necessary for theoretical studies, enzyme engineering, drug design, and so on. The most existing methods use the multiple sequence alignment. They have the limitations in prediction accuracy due to the family sequence divergence and ligand-based grouping. We developed a new method SPrOS (Specificity Projection On Sequence) for estimating the specificity of residues to user-defined groups. SPrOS compares the sequence segments from the test protein and training proteins. Contrary to other segment-comparison approaches extracting the string motifs, SPrOS calculates the scores for single positions by the similarity of their surroundings. The method was evaluated on the simulated sequences and real protein families. The high-prediction accuracy was achieved for simulated sequences, in which SPrOS detected specific positions not predicted with the alignment-based method. For bacterial transcription factors (LacI/GalR) clearly divided into functional groups, the predicted specific residues corresponded to the published experimental data. In a more complicated case of protein kinases classified by inhibitor specificity, the positions predicted with high significance were located in ligand-binding areas. As the ligand specificity is not necessary coincided with phylogeny, evolutionary-coupled mutations could disturb the detection of ligand-specific residues. Excluding proximate homologs of the test protein kinase from the training set, we improved the prediction of the ligand-specific residues. The SPrOS is available at http://www.way2drug.com/spros/

In-hospital mortality after hip fracture by treatment setting.

BACKGROUND: Where patients with hip fracture undergo treatment may influence their outcome. We compared the risk of in-hospital death after hip fracture by treatment setting in Canada. METHODS: We examined all discharge abstracts from the Canadian Institute for Health Information with diagnosis codes for hip fracture involving patients 65 years and older who were admitted to hospital with a nonpathological first hip fracture between Jan. 1, 2004, and Dec. 31, 2012, in Canada (excluding Quebec). We compared the risk of in-hospital death, overall and after surgery, between teaching hospitals and community hospitals of various bed capacities, accounting for variation in length of stay. RESULTS: Compared with the number of deaths per 1000 admissions at teaching hospitals, there were an additional 3 (95% confidence interval [CI] 1-6), 14 (95% CI 10-18) and 43 (95% CI 35-51) deaths per 1000 admissions at large, medium and small community hospitals, respectively. For the risk of in-hospital death overall, the adjusted odds ratios (ORs) were 1.05 (95% CI 0.99-1.11), 1.16 (95% CI 1.09-1.24) and 1.44 (95% CI 1.31-1.57) at large, medium and small community hospitals, respectively, compared with teaching hospitals. For the risk of postsurgical death in hospital, the adjusted ORs were 1.06 (95% CI 1.00-1.13), 1.13 (95% CI 1.04-1.23) and 1.18 (95% CI 0.87-1.60) at large, medium and small community hospitals, respectively. INTERPRETATION: Compared with teaching hospitals, the risk of in-hospital death among patients with hip fracture was higher at medium and small community hospitals, and the risk of in-hospital death after surgery was higher at medium community hospitals. No differences were found between teaching and large community hospitals. Future research should examine the role of volume, demand and bed occupancy for observed differences.

The effect of early in-hospital medication review on health outcomes: a systematic review.

AIMS: Adverse drug events are an important cause of emergency department visits, unplanned admissions and prolonged hospital stays. Our objective was to synthesize the evidence on the effect of early in-hospital pharmacist-led medication review on patient-oriented outcomes based on observed data. METHODS: We systematically searched eight bibliographic reference databases, electronic grey literature, medical journals, conference proceedings, trial registries and bibliographies of relevant papers. We included studies that employed random or quasi-random methods to allocate subjects to pharmacist-led medication review or control. Medication review had to include, at a minimum, obtaining a best possible medication history and reviewing medications for appropriateness and adverse drug events. The intervention had to be initiated within 24 h of emergency department presentation or 72 h of admission. We extracted data in duplicate and pooled outcomes from clinically homogeneous studies of the same design using random effects meta-analysis. RESULTS: We retrieved 4549 titles of which seven were included, reporting the outcomes of 3292 patients. We pooled data from studies of the same design, and found no significant differences in length of hospital admission (weighted mean difference [WMD] -0.04 days, 95% confidence interval [CI] -1.63, 1.55), mortality (odds ratio [OR] 1.09, 95% CI 0.69, 1.72), readmissions (OR 1.15, 95% CI 0.81, 1.63) or emergency department revisits at 3 months (OR 0.60, 95% CI 0.27, 1.32). Two large studies reporting reductions in readmissions could not be included in our pooled estimates due to differences in study design. CONCLUSIONS: Wide confidence intervals suggest that additional research is likely to influence the effect size estimates and clarify the effect of medication review on patient-oriented outcomes. This systematic review failed to identify an effect of pharmacist-led medication review on health outcomes.

Classifying outcomes of care for injured patients.

Many trauma survivors face challenges of impaired functioning, limited activities and reduced participation. Recovery from injury after acute care, therefore, becomes an important public health issue. This commentary discusses a framework for evaluating outcomes of acute care.

Prediction of viral protease inhibitors using proteochemometrics approach.

Being widely accepted tools in computational drug search, the (Q)SAR methods have limitations related to data incompleteness. The proteochemometrics (PCM) approach expands the applicability area by using description for both protein and ligand structures. The PCM algorithms are urgently required for the development of new antiviral agents. We suggest the PCM method using the TLMNA descriptors, combining the MNA descriptors of ligands and protein sequence N-grams. Our method was validated on the viral chymotrypsin-like proteases and their ligands. We have developed an original protocol allowing us to collect a comprehensive set of 15 protein sequences and more than 9000 ligands from the ChEMBL database. The N-grams were derived from the 3D-based alignment, accurately superposing ligand-binding regions. In testing the ligand set in SAR mode with MNA descriptors, an accuracy above 0.95 was determined that shows the perspective of the antiviral drug search in virtual chemical libraries. The effective PCM models were built with the TLMNA descriptor. The strong validation procedure with pair exclusion simulated the prediction of interactions between the new ligands and new targets, resulting in accuracy estimation up to 0.89. The PCM approach shows slightly lower accuracy caused by more uncertainty compared with SAR, but it overcomes the problem of data incompleteness.