bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postural stability in the cognitively impaired elderly: A systematic review of the literature
Authors: Cieślik Błażej , Jaworska Lilianna , Szczepańska-Gieracha Joanna 
Published: August 2016

Introduction The aim of this study was to review the literature and critically analyse publications connecting cognitive impairment with postural stability. Methods Four electronic databases were searched. The inclusion criteria comprised the relation between the process of maintaining balance and cognitive impairment. Results Of the 153 selected articles, 15 met the inclusion criteria. In 83% of publications, cognitive status was determined with the use of the Mini-Mental State Examination. In eight publications, postural stability was examined using force plates. Other methods used to test the balance were functional tests, i.e. the Berg Balance Scale or the Balance Evaluation Systems Test. Conclusion As the choice of methodology varies significantly, it is difficult to attempt an objective comparison between different studies. There is a clear need for the normalisation of methods used to assess the degree of dementia and to assess postural stability among this group of people.
Advanced Imaging in Osteoarthritis
Authors: Li Qi , Amano Keiko , Link Thomas M. , Ma C. Benjamin 
Published: August 2016

Context: Radiography is widely accepted as the gold standard for diagnosing osteoarthritis (OA), but it has limitations when assessing early stage OA and monitoring progression. While there are improvements in the treatment of OA, the challenge is early recognition. Evidence Acquisition: MEDLINE and PubMed as well as professional orthopaedic and imaging websites were reviewed from 2006 to 2016. Study Design: Clinical review. Level of Evidence: Level 4. Results: Magnetic resonance imaging (MRI) can provide the most comprehensive assessment of joint injury and OA with the advantages of being noninvasive and multiplanar with excellent soft tissue contrast. However, MRI is expensive, time consuming, and not widely used for monitoring OA clinically. Computed tomography (CT) and CT arthrography (CTA) can also be used to evaluate OA, but these are also invasive and require radiation exposure. Ultrasound is particularly useful for evaluation of synovitis but not for progression of OA. Conclusion: MRI, CT, and CTA are available for the diagnosis and monitoring of OA. Improvement in techniques and decrease in cost can allow some of these modalities to be effective methods of detecting early OA.
Characterization of Articular Cartilage Recovery and Its Correlation with Optical Response in the Near-Infrared Spectral Range
Authors: Afara Isaac Oluwaseun , Singh Sanjleena , Moody Hayley , Zhang Lihai , Oloyede Adekunle 
Published: August 2016

Objectives: In this study, we examine the capacity of a new parameter, based on the recovery response of articular cartilage, to distinguish between healthy and damaged tissues. We also investigate whether or not this new parameter correlates with the near-infrared (NIR) optical response of articular cartilage. Design: Normal and artificially degenerated (proteoglycan-depleted) bovine cartilage samples were nondestructively probed using NIR spectroscopy. Subsequently they were subjected to a load and unloading protocol, and the recovery response was logged during unloading. The recovery parameter, elastic rebound ( ER), is based on the strain energy released as the samples underwent instantaneous elastic recovery. Results: Our results reveal positive relationship between the rebound parameter and cartilage proteoglycan content (normal samples: 2.20 ± 0.10 N mm; proteoglycan-depleted samples: 0.50 ± 0.04 N mm for 1 hour of enzymatic treatment and 0.13 ± 0.02 N mm for 4 hours of enzymatic treatment). In addition, multivariate analysis using partial least squares regression was employed to investigate the relationship between ER and NIR spectral data. The results reveal significantly high correlation ( R2cal = 98.35% and R2val = 79.87%; P < 0.0001), with relatively low error (14%), between the recovery and optical response of cartilage in the combined NIR regions 5,450 to 6,100 cm−1 and 7,500 to 12,500 cm−1. Conclusion: We conclude that ER can indicate the mechanical condition and state of health of articular cartilage. The correlation of ER with cartilage optical response in the NIR range could facilitate real-time evaluation of the tissue’s integrity during arthroscopic surgery and could also provide an important tool for cartilage assessment in tissue engineering and regeneration research.
Biomechanical Evaluation of Posterior Cruciate Ligament Reconstruction With Quadriceps Versus Achilles Tendon Bone Block Allograft
Authors: Forsythe Brian , Haro Marc S. , Bogunovic Ljiljana , Collins Michael J. , Arns Thomas A. , Trella Katie J. , Shewman Elizabeth F. , Verma Nikhil N. , Bach Bernard R. 
Published: August 2016

Background: Long-term studies of posterior cruciate ligament (PCL) reconstruction suggest that normal stability is not restored in the majority of patients. The Achilles tendon allograft is frequently utilized, although recently, the quadriceps tendon has been introduced as an alternative option due to its size and high patellar bone density. Purpose/Hypothesis: The purpose of this study was to compare the biomechanical strength of PCL reconstructions using a quadriceps versus an Achilles allograft. The hypothesis was that quadriceps bone block allograft has comparable mechanical properties to those of Achilles bone block allograft. Study Design: Controlled laboratory study. Methods: Twenty-nine fresh-frozen cadaveric knees were assigned to 1 of 3 groups: (1) intact PCL, (2) PCL reconstruction with Achilles tendon allograft, or (3) PCL reconstruction with quadriceps tendon allograft. After reconstruction, all supporting capsular and ligamentous tissues were removed. Posterior tibial translation was measured at neutral and 20° external rotation. Each specimen underwent a preload, 2 cyclic loading protocols of 500 cycles, then load to failure. Results: Construct creep deformation was significantly lower in the intact group compared with both Achilles and quadriceps allograft ( P = .008). The intact specimens reached the greatest ultimate load compared with both reconstructions (1974 ± 752 N, P = .0001). The difference in ultimate load for quadriceps versus Achilles allograft was significant ( P = .048), with the quadriceps group having greater maximum force during failure testing. No significant differences were noted between quadriceps versus Achilles allograft for differences in crosshead excursion during cyclic testing (peak-valley [P-V] extension stretch), creep deformation, or stiffness. Construct stiffness measured during the failure test was greatest in the intact group (117 ± 9 N/mm, P = .0001) compared with the Achilles (43 ± 11 N/mm) and quadriceps (43 ± 7 N/mm) groups. Conclusion: While the quadriceps trended to be a stronger construct with a greater maximum load and stiffness required during load to failure, only maximum force in comparison with the Achilles reached statistical significance. Quadriceps and Achilles tendon allografts had similar other biomechanical characteristics when used for a PCL reconstruction, but both were inferior to the native PCL. Clinical Relevance: The quadriceps tendon is a viable graft option in PCL reconstruction as it exhibits a greater maximum force and is otherwise comparable to the Achilles allograft. These findings expand allograft availability in PCL reconstruction.
BAMQL: a query language for extracting reads from BAM files
Authors: Masella Andre P. , Lalansingh Christopher M. , Sivasundaram Pragash , Fraser Michael , Bristow Robert G. , Boutros Paul C. 
Published: August 2016

Abstract
Background
It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream using SAMtools, parses and filters the lines using AWK, then repacks them using SAMtools. This process is tedious and error-prone. In particular, when working with many columns of data, mix-ups are common and the bit field containing the flags is unintuitive. There are several libraries for reading BAM files, such as for Perl and for Python. Both allow access to the BAM’s read information and can filter reads, but require substantial boilerplate code; this is high overhead for mostly ad hoc filtering.

Results
We have created a query language that gathers reads using a collection of predicates and common logical connectives. Queries run faster than equivalents and can be compiled to native code for embedding in larger programs.

Conclusions
BAMQL provides a user-friendly, powerful and performant way to extract subsets of BAM files for ad hoc analyses or integration into applications. The query language provides a collection of predicates beyond those in SAMtools, and more flexible connectives.
Serum starvation-induced cell cycle synchronization stimulated mouse rDNA transcription reactivation during somatic cell reprogramming into iPSCs
Authors: Zhao Qiaoshi , Wu Yanshuang , Shan Zhiyan , Bai Guangyu , Wang Zhendong , Hu Jing , Liu Li , Li Tong , Shen Jingling , Lei Lei 
Published: August 2016

Abstract
Background
rDNA, the genes encoding ribosomal RNA (rRNA), is highly demanded for ribosome production and protein synthesis in growing cells such as pluripotent stem cells. rDNA transcription activity varies between cell types, metabolism conditions, and specific environmental challenges. Embryonic stem cells (ESCs), partially reprogrammed cells, and somatic cells reveal different epigenetic signatures, including rDNA epigenetic marks. rDNA epigenetic characteristic resetting is not quite clear during induced pluripotent stem cell (iPSC) generation. Little is known that whether the different rDNA epigenetic status in donor cells will result in different rDNA transcription activities, and furthermore affect reprogramming efficiency.

Methods
We utilized serum starvation-synchronized mouse embryonic fibroblasts (MEFs) to generate S-iPSCs. Both MEFs and serum-refeeding MEFs (S-MEFs) were reprogrammed to a pluripotent state. rDNA-related genes, UBF proteins, and rDNA methylation levels were detected during the MEF and S-MEF cell reprogramming process.

Results
We demonstrated that, after transient inhibition, retroviral induced rRNA transcriptional activity was reprogrammed towards a pluripotent state. Serum starvation would stimulate rDNA transcription reactivation during somatic cell reprogramming. Serum starvation improved the methylation status of donor cells at rRNA gene promoter regions.

Conclusions
Our results provide insight into regulation of rDNA transcriptional activity during somatic cell reprogramming and allow for comparison of rDNA regulation patterns between iPSCs and S-iPSCs. Eventually, regulation of rDNA transcriptional activity will benefit partially reprogrammed cells to overcome the epigenetic barrier to pluripotency.
Human umbilical cord-derived mesenchymal stem cells protect against experimental colitis via CD5+ B regulatory cells
Authors: Chao Kang , Zhang Shenghong , Qiu Yun , Chen Xiaoyong , Zhang Xiaoran , Cai Chuang , Peng Yanwen , Mao Ren , Pevsner-Fischer Meirav , Ben-horin Shomron , Elinav Eran , Zeng Zhirong , Chen Baili , He Yao , Xiang Andy Peng , Chen Minhu 
Published: August 2016

Abstract
Background
To clarify the effect of human umbilical cord-derived mesenchymal stem cell (hUC-MSCs) treatment on colitis and to explore the role of CD5+ B cells in MSC therapy.

Methods
The trinitrobenzenesulfonic acid (TNBS)-induced colitis mouse model was used. HUC-MSCs were transferred peritoneally. Survival rates, colitis symptoms, and macroscopic and histologic scores were evaluated. CD4+ T helper (Th) cell subgroups and CD5+ regulatory B cell (Bregs) in lymphocytes were quantitated by flow cytometry. Cytokine levels were detected by ELISA and Bio-plex. CD5+ B cells were isolated for in vitro co-culture and adaptive transfer.

Results
HUC-MSC treatment alleviated TNBS-induced colitis by increasing survival rates, relieving symptoms, and improving macroscopic and histologic scores. Labeled hUC-MSCs were located in the inflamed areas of colitis mice. Increases in regulatory T cells (Tregs) and CD5+ B cells and decreases in Th1 cells, Th17 cells, and several pro-inflammatory cytokines were observed with hUC-MSC treatment. After adaptive transfer, CD5+ B cells, which were located mainly in the peritoneal lavage fluid, improved TNBS-induced colitis by correcting Treg/Th1/Th17 imbalances. CD5+ B cells also inhibited T-cell proliferation and produced interleukin (IL)-10.

Conclusions
HUC-MSCs protected against experimental colitis by boosting the numbers of CD5+ B cells and IL-10-producing CD5+ Bregs, and correcting Treg/Th17/Th1 imbalances.
Cost-effectiveness of telehealth for patients with depression: evidence from the Healthlines randomised controlled trial
Authors: Dixon Padraig , Hollinghurst Sandra , Edwards Louisa , Thomas Clare , Foster Alexis , Davies Ben , Gaunt Daisy , Montgomery Alan A. , Salisbury Chris 
Published: August 2016

BackgroundDepression is a prevalent long-term condition that is associated with substantial resource use. Telehealth may offer a cost-effective means of supporting the management of people with depression.AimsTo investigate the cost-effectiveness of a telehealth intervention (‘Healthlines’) for patients with depression.MethodA prospective patient-level economic evaluation conducted alongside a randomised controlled trial. Patients were recruited through primary care, and the intervention was delivered via a telehealth service. Participants with a confirmed diagnosis of depression and PHQ-9 score ≥10 were recruited from 43 English general practices. A series of up to 10 scripted, theory-led, telephone encounters with health information advisers supported participants to effect a behaviour change, use online resources, optimise medication and improve adherence. The intervention was delivered alongside usual care and was designed to support rather than duplicate primary care. Cost-effectiveness from a combined health and social care perspective was measured by net monetary benefit at the end of 12 months of follow-up, calculated from incremental cost and incremental quality-adjusted life years (QALYs). Cost–consequence analysis included cost of lost productivity, participant out-of-pocket expenditure and the clinical outcome.ResultsA total of 609 participants were randomised – 307 to receive the Healthlines intervention plus usual care and 302 to receive usual care alone. Forty-five per cent of participants had missing quality of life data, 41% had missing cost data and 51% of participants had missing data on either cost or utility, or both. Multiple imputation was used for the base-case analysis. The intervention was associated with incremental mean per-patient National Health Service/personal social services cost of £168 (95% CI £43 to £294) and an incremental QALY gain of 0.001 (95% CI −0.023 to 0.026). The incremental cost-effectiveness ratio was £132 630. Net monetary benefit at a cost-effectiveness threshold of £20 000 was –£143 (95% CI –£164 to –£122) and the probability of the intervention being cost-effective at this threshold value was 0.30. Productivity costs were higher in the intervention arm, but out-of-pocket expenses were lower.ConclusionsThe Healthlines service was acceptable to patients as a means of condition management, and response to treatment after 4 months was higher for participants randomised to the intervention. However, the positive average intervention effect size was modest, and incremental costs were high relative to a small incremental QALY gain at 12 months. The intervention is not likely to be cost-effective in its current form.
Do Gender and Business Trainings Affect Business Outcomes? Experimental Evidence from Vietnam
Authors: Bulte Erwin , Lensink Robert , Vu Nhung 
Published: August 2016

We use a randomized control trial to evaluate the impact of a business training for female clients of a microfinance institution in northern Vietnam, and we consider the impact on (i) business knowledge, (ii) practices, and (ii) outcomes, as well as (iv) firm entry and exit decisions. In addition, we vary the nature of the intervention by inviting husbands to participate in the trainings for a subsample of our respondents. To gauge both short-term and medium-term effects, we combine data from two separate postintervention surveys. We find evidence of economically substantive impacts on knowledge, practices, and outcomes, and on the extensive margin (entry and exit). We also document that it takes time for the “downstream” outcomes of the trainings to materialize; although we find evidence of medium-term effects, no such evidence exists for the short term. Inviting husbands to participate in the trainings does not affect any of our knowledge or practice measures, but we document weak evidence for differential impact on (agricultural) sales and profits. Data, as supplemental material, are available at http://dx.doi.org/10.1287/mnsc.2016.2472 . This paper was accepted by Uri Gneezy, behavioral economics.
Do Bags Fly Free? An Empirical Analysis of the Operational Implications of Airline Baggage Fees
Authors: Nicolae Mariana , Arıkan Mazhar , Deshpande Vinayak , Ferguson Mark 
Published: August 2016

In 2008, the majority of U.S. airlines began charging for the second checked bag, and then for the first checked bag. One of the often cited reasons for this action by the airlines’ executives was that this would influence customers to travel with less baggage and thus improve cost and operational performance. A popular customer belief, however, is that airline departure delays got worse due to an increase and size of customer carry-on baggage. A notable exception to the charging for checked bags trend was Southwest Airlines, which turned their resistance to this practice into a “Bags Fly Free” marketing campaign. Using a publicly available database of the airlines’ departure performance, we investigate whether the implementation of checked bag fees was really associated with better operational performance metrics. At the aggregate level, using all publicly recorded U.S. flights from May 1, 2007, to May 1, 2009, we find that the airlines that began charging for checked bags saw a significant relative improvement in their on-time departure performance in the time periods after the baggage fees were implemented. Surprisingly, we also find that airlines that did not charge for checked bags also saw an improvement, although not as big, when competing airlines flying the same origin-destination city markets implemented the fees. The improvement in on-time departure performance was the largest for flights during peak evening departure time blocks. This paper was accepted by Serguei Netessine, operations management.
Using Machine Learning and Natural Language Processing Algorithms to Automate the
Evaluation of Clinical Decision Support in Electronic Medical Record Systems
Authors: Szlosek Donald A. , Ferretti Jonathan M. 
Published: August 2016

Introduction: As the number of clinical decision support systems incorporated into
electronic medical records increases, so does the need to evaluate their effectiveness.
The use of medical record review and similar manual methods for evaluating decision
rules is laborious and inefficient. Here we use machine learning and natural language
processing (NLP) algorithms to accurately evaluate a clinical decision support rule
through an electronic medical record system and compare it against manual
evaluation.Methods: Modeled after the electronic medical record system EPIC at Maine
Medical Center, we developed a dummy dataset containing physician notes in free text for
3621 artificial patients records undergoing a head computed tomography scan for mild
traumatic brain injury after the incorporation of an electronic best practice approach.
We validated the accuracy of the BPA using three machine learning algorithms (SVC,
DecisionTreeClassifier; KNeighborsClassifier) by comparing their accuracy for
adjudicating the occurrence of a mild traumatic brain injury against manual review. We
then used the best of the three algorithms to evaluate the effectiveness of the BPA and
compared the algorithm’s evaluation of the BPA to that of manual review.Results: The
electronic best practice approach was found to have a sensitivity of 98.8%
(96.83-100.0), specificity of 10.3%, PPV = 7.3%, and NPV = 99.2% when reviewed manually
by abstractors. Though all the machine learning algorithms were observed to have a high
level of prediction, the SVC displayed the highest with a sensitivity 93.33%
(92.49-98.84) , specificity of 97.62% (96.53-98.38), PPV = 50.00, NPV = 99.83. The SVC
algorithm was observed to have a sensitivity of 97.9% (94.7-99.86), specificity 10.30%,
PPV 7.25%, and NPV 99.2% for evaluating the best practice approach, after accounting for
17 cases (0.66%) where the patient records had to be reviewed manually due to the NPL
systems inability to capture the proper diagnosis.Discussion: Evaluation of clinical
decision support systems incorporated into electronic medical records can be achieved in
an automatic fashion by using natural language processing and machine learning
techniques.
Venous thromboembolism after total knee replacement or total hip replacement: what can be learnt from root-cause analysis?
Authors: Benjamin S , Warwick D 
Published: August 2016

INTRODUCTION Because of the high risk of venous thromboembolism (VTE) in total hip replacement (THR) and total knee replacement (TKR), guidelines are used widely to enhance effective (yet safe) prophylaxis. If patients develop VTEs despite use of such guidelines, then the reasons are that the guidelines were: (i) followed but the VTE occurred anyway; (ii) not implemented appropriately. All VTEs are assessed routinely by root-cause analysis (RCA). METHODS The records and subsequent RCA reports for each patient who experienced clinically significant VTE after THR or TKR were reviewed. We established adherence to the guidelines (deemed to be ‘unavoidable’ with scope to improve the guidelines) and non-adherence (deemed to be ‘avoidable’ with scope to improve implementation). RESULTS Of 2,214 patients undergoing THR (n=1,330) or TKR (n=884), 25 (1.13%) experienced VTE. Four THR patients experienced VTE (2 of which were avoidable) and 21 TKR patients experienced VTE (5 of which were avoidable). There were significantly more VTEs in TKR patients than THR patients (p<0.0001). CONCLUSIONS A proportion of patients will experience VTE even if guidelines are followed (a baseline effect). Administration of chemical prophylaxis earlier might reduce this baseline effect further. This approach should be taken cautiously with due respect for the alternative risk of bleeding. Improvement in hospital routine may reduce the risk of VTE yet further.