bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Lived Environment Life Quality Model for institutionalized people with dementia
Authors: Wood Wendy , Lampe Jenna L. , Logan Christina A. , Metcalfe Amy R. , Hoesly Beth E. 
Published: July 2016

Background. There is a need for a conceptual practice model that explicates ecological complexities involved in using occupation to optimize the quality of life of institutionalized people with dementia. Purpose. This study aimed to prepare the Lived Environment Life Quality Model, a dementia-specific conceptual practice model of occupational therapy in institutional facilities, for publication and application to practice. Method. Interviews and focus groups with six expert occupational therapists were subjected to qualitative content analysis to confirm, disconfirm, and further develop the model. Findings. The model’s lived-environment domain as the focus of assessment and intervention was extensively confirmed, and its quality-of-life domain as the focus of intervention goals and outcomes was both confirmed and further developed. Implications. As confirmed in this study, the Lived Environment Life Quality Model is a client-centred, ecologically valid, and occupation-focused guide to optimizing quality of life of institutionalized adults with dementia in present moments and progressively over time.
The association between sensory processing styles and mindfulness
Authors: Hebert Karen R 
Published: July 2016

Introduction Mindfulness is associated with psychological wellbeing and quality of life. The focus on body awareness in definitions of mindfulness suggests that an individual’s sensory processing pattern may influence mindfulness abilities. Therefore, this study seeks to examine the relationship between sensory processing styles and multiple aspects of mindfulness including components of attention, awareness, and acceptance in healthy adults. Method 151 participants, aged 18 to 60 (mean 25.24 ± 8.8), completed the Adolescent/Adult Sensory Profile, mindful attention and awareness scale, and cognitive and affective mindfulness scale. Findings Aspects of mindfulness associated with attention and awareness were significantly negatively related to sensory processing patterns associated with passive behavioral strategies (low registration and sensory sensitivity). Conclusion Individuals whose sensory processing patterns are characterized by poor awareness experience more mind wandering and distraction in daily life. Occupational therapists should consider mindfulness techniques when treating individuals with sensory processing disorders. In addition, information about sensory processing styles should be incorporated into relaxation and mindfulness-based interventions.
Diagnosis of primary headache in children younger than 6 years: A clinical challenge
Authors: Torriero Roberto , Capuano Alessandro , Mariani Rosanna , Frusciante Roberto , Tarantino Samuela , Papetti Laura , Vigevano Federico , Valeriani Massimiliano 
Published: July 2016

Background Criteria defined by the International headache Society are commonly used for the diagnosis of the different headache types in both adults and children. However, some authors have stressed some limits of these criteria when applied to preschool age. Objective Our study aimed to describe the characteristics of primary headaches in children younger than 6 years and investigate how often the International Classification of Headache Disorders (ICHD) criteria allow a definitive diagnosis. Methods This retrospective study analysed the clinical feature of 368 children younger than 6 years with primary headache. Results We found that in our patients the percentage of undefined diagnosis was high when either the ICHD-II or the ICHD-III criteria were used. More than 70% of our children showed a duration of their attacks shorter than 1 hour. The absence of photophobia/phonophobia and nausea/vomiting significantly correlate with tension-type headache (TTH) and probable TTH. The number of first-degree relatives with migraine was positively correlated to the diagnosis of migraine in the patients ( p < 0.001). Conclusions Our study showed that the ICHD-III criteria are difficult to use in children younger than 6 years. The problem is not solved by the reduction of the lowest duration limit for the diagnosis of migraine to 1 hour, as was done in the ICHD-II.
Morphologic Characteristics and Strength of the Hamstring Muscles Remain Altered at 2 Years After Use of a Hamstring Tendon Graft in Anterior Cruciate Ligament Reconstruction
Authors: Konrath Jason M. , Vertullo Christopher J. , Kennedy Ben A. , Bush Hamish S. , Barrett Rod S. , Lloyd David G. 
Published: July 2016

Background: The hamstring tendon graft used in anterior cruciate ligament (ACL) reconstruction has been shown to lead to changes to the semitendinosus and gracilis musculature. Hypothesis: We hypothesized that (1) loss of donor muscle size would significantly correlate with knee muscle strength deficits, (2) loss of donor muscle size would be greater for muscles that do not experience tendon regeneration, and (3) morphological adaptations would also be evident in nondonor knee muscles. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Twenty participants (14 men and 6 women, mean age 29 ± 7 years, mean body mass 82 ± 15 kg) who had undergone an ACL reconstruction with a hamstring tendon graft at least 2 years previously underwent bilateral magnetic resonance imaging and subsequent strength testing. Muscle and tendon volumes, peak cross-sectional areas (CSAs), and lengths were determined for 12 muscles and 6 functional muscle groups of the surgical and contralateral limbs. Peak isokinetic concentric strength was measured in knee flexion/extension and internal/external tibial rotation. Results: Only 35% of the patients showed regeneration of both the semitendinosus and gracilis tendons. The regenerated tendons were longer with larger volume and CSA compared with the contralateral side. Deficits in semitendinosus and gracilis muscle size were greater for muscles in which tendons did not regenerate. In addition, combined hamstring muscles (semitendinosus, semimembranosus, and biceps femoris) and combined medial knee muscles (semitendinosus, semimembranosus, gracilis, vastus medialis, medial gastrocnemius, and sartorius) on the surgical side were reduced in volume by 12% and 10%, respectively. A 7% larger volume was observed in the surgical limb for the biceps femoris muscle and corresponded with a lower internal/external tibial rotation strength ratio. The difference in volume, peak CSA, and length of the semitendinosus and gracilis correlated significantly with the deficit in knee flexion strength, with Pearson correlations of 0.51, 0.57, and 0.61, respectively. Conclusion: The muscle-tendon properties of the semitendinosus and gracilis are substantially altered after harvesting, and these alterations may contribute to knee flexor weakness in the surgical limb. These deficits are more pronounced in knees with tendons that do not regenerate and are only partially offset by compensatory hypertrophy of other hamstring muscles.
Genetic selection pressure in TLR9 gene may enforce risk for SLE in Indian Tamils
Authors: Yusuf J H , Kaliyaperumal D , Jayaraman M , Ramanathan G , Devaraju P 
Published: July 2016

Objectives Lupus is a classical systemic autoimmune disease with genetics as one of the well known causative factors for the disease pathogenesis. Toll-like receptors are the major pattern recognition receptors associated with innate immunity and also act as an interface with the adaptive immunity. Genetic polymorphisms in genes encoding TLRs were implicated in the development of infections, malignancies and autoimmune diseases. TLR9 is a member of TLR family, and recognizes the CpG DNA motifs of pathogens. Though the incidence rate of lupus in Asians was reported to be low (30 − 50/100,000 population), poor disease prognosis due to higher incidence of renal complications and aggressive disease worsens the scenario. The ability of TLR9 to detect and elicit an immune response against double-stranded DNA makes TLR9 a relevant factor to be tested for its association with the clinical and serological phenotypes of lupus. However, lack of relevant genetic data on normative frequencies of the TLR9 (rs187084) polymorphism may serve as a constraint to derive the sample size to conduct case control association studies. Hence this study was conducted to establish the normative frequency of TLR9 (rs187084) polymorphism in Indian Tamils. Materials and methods The TLR9 (rs187084) polymorphism was screened in South Indian Tamils ( n = 208) by PCR-RFLP. Results and discussion We observed a higher occurrence of the mutant allele (65%) in South Indian Tamils. No gender disparity with respect to the mutant allele frequency was observed. The higher incidence of mutant allele in both genders suggests that this population had undergone a genetic selection pressure as an evolutionary genetic measure to withstand the prevailing endemic infections like TB and malaria. Though the enhanced expression of TLR9 was protective against infections, it may also influence the development of autoimmune diseases. Conclusion The higher incidence of theTLR9 (rs187084) over-expression mutation in Indian Tamils is suggestive of a genetic adaptation or selection pressure to withstand the prevailing endemic infectious and parasitic diseases. However, this genetic adaptation poses a greater risk to develop autoimmune diseases like SLE etc through complex gene environment interactions. The normative frequency of the TLR9 (rs187084) polymorphism established in our population could now be used to define the sample size for future case control studies.
Usefulness of acute phase proteins in differentiating between feline infectious peritonitis and other diseases in cats with body cavity effusions
Authors: Hazuchova Katarina , Held Susanne , Neiger Reto 
Published: July 2016

Objectives The aim of this study was to evaluate the measurement of acute phase proteins (APPs) as a diagnostic tool to differentiate between feline infectious peritonitis (FIP) and other diseases in cats with body cavity effusions. Methods Cats with pleural, abdominal or pericardial effusion were prospectively enrolled. Cats were classified as having or not having FIP based on immunohistochemistry (if available) or a sophisticated statistical method using machine learning methodology with concepts from game theory. Cats without FIP were further subdivided into three subgroups: cardiac disease, neoplasia and other diseases. Serum amyloid A (SAA), haptoglobin (Hp) and α1-acid glycoprotein (AGP) were measured in serum and effusion, using assays previously validated in cats. Results Serum and effusion samples were available for the measurement of APPs from 88 and 67 cats, respectively. Concentrations of the APPs in serum and effusion were significantly different in cats with and without FIP ( P <0.001 for all three APPs). The best APP to distinguish between cats with and without FIP was AGP in the effusion; a cut-off value of 1550 µg/ml had a sensitivity and specificity of 93% each for diagnosing FIP. Conclusions and relevance AGP, particularly if measured in effusion, was found to be useful in differentiating between FIP and other diseases, while SAA and Hp were not. The concentration of all three APPs in some diseases (eg, septic processes, disseminated neoplasia) was as high as in cats with FIP; therefore, none of these can be recommended as a single diagnostic test for FIP.
Clinical, histological and prognostic features of a novel nail-bed lesion of cats: 41 cases
Authors: Dobromylskyj Melanie J , Fernandes Rebecca A , French Adrienne , Pocknell Ann M , Smith Ken C 
Published: July 2016

Objectives There is a distinct subset of lesions arising on the digits of cats, located at or close to the nail-bed epithelium, which are typically composed of proliferative fibroblast-like cells, multinucleate giant cells and areas of osseous metaplasia, but currently there is no published literature detailing the clinical or histological features of these lesions. Methods This study identified 41 such cases from two large commercial diagnostic laboratories and assessed various histological and clinical features; 22 cases had additional follow-up data available. Results All masses in this study were exophytic, variably inflamed, contained large numbers of spindle cells and had areas of capillary formation. The majority also had areas of ulceration, multinucleate giant cells and osseous metaplasia. The mitotic count was variable, but mitoses were confined to the fibroblast-like cells. Male cats appeared predisposed and the second digit was the most commonly affected. Conclusions and relevance These distinctive lesions arising on the digits of cats had potential for local recurrence but metastasis was not reported. Based on these clinical and histological features, the masses in this study appear most similar to giant cell reparative granulomas, and trauma, injury to the nail or nail-bed and nail-bed infections may potentially contribute to their development.
Listeria rhombencephalitis mimicking a demyelinating event in an immunocompetent young patient
Authors: Décard Bernhard F , Thöne Jan , Haghikia Aiden , Börnke Christian , Anders Agnes , Lukas Carsten , Gold Ralf 
Published: July 2016

Background: Listeriosis caused by listeria monocytogenes (LM) is a potentially lethal foodborne infection of the central nervous system (CNS) and the third most common cause of bacterial meningitis. Foods most commonly implicated are soft cheeses, raw or ready-to-eat meat and pre-processed foods. The incubation time is between 11 and 70 days. Rarely LM rhombencephalitis (RE) can occur, which typically has a biphasic course with non- specific prodromal symptoms like fever, malaise, fatigue, headache, nausea and vomiting followed by cranial nerve palsies, ataxia and hemi- or tetraparesis. Objective: To report a 31-year old immunocompetent female developing a severe abscessing RE caused by LM, which was initially assessed as a relapse after a clinically isolated syndrome (CIS). Methods: Case report. Results: Patients with CIS or multiple sclerosis, who present with brainstem symptoms should be evaluated carefully. The presence of clinical and paraclinical red flags in the diagnostic evaluation of a suspected CNS white matter disease should raise the awareness of clinicians for potential differential diagnoses.
Postoperative Urinary Leakage Following Partial Nephrectomy for Renal Mass: Risk Factors and a Proposed Algorithm for the Diagnosis and Management
Authors: Erlich T. , Abu-Ghanem Y. , Ramon J. , Mor Y. , Rosenzweig B. , Dotan Z. 
Published: July 2016

Objectives: To evaluate the current incidence, risk factors, management, and long-term follow-up of urinary leakage following partial nephrectomy, in order to propose an algorithm for diagnosis and evaluation of postoperative urinary leakage. Materials and Methods: The study included 752 patients who underwent elective partial nephrectomies for renal masses between the years 1988 and 2013. Patients’ demographics, clinico-pathologic variables, and operative details were collected retrospectively. The associations between urinary leakage and patients’ variables were assessed by univariate and multivariate analyses. Results: Of the 752 patients, 21 (2.8%) experienced urinary leakage; 4 of the 21 patients with urinary leakage had spontaneous resolution, 1 patient underwent nephrectomy, and 16 patients were treated by retrograde ureteral stents insertion. One of them necessitated insertion of an additional percutaneous nephrostomy and another one deserved concomitant percutaneous drainage of a perirenal urinoma. The average period of time that elapsed from the operation until the insertion of stent was 8.5 ± 4.5 days. Stents were removed 68 ± 20.5 days postoperatively. None of the patients had either persistent or repeated leakage. On univariate analysis, hilar renal masses (p < 0.04) and higher preoperative creatinine levels (p < 0.01) were found to be associated with higher rates of urinary leakage. None of these variables was significant on a multivariate analysis. Review of the urinary leakage rate over time revealed it has been constantly decreasing over time, from 4% in early cases to 1.3% among the most recent ones. Conclusion: None of the preoperative variables that were examined in this study was significantly associated with increased risk of urinary leakage. However, cumulative surgical experience was associated with lower rates of urinary leakage, suggesting that the decrease in its incidence is related to the improved surgical skills, rather than to differences in tumors’ or patients’ characteristics.
Clinical impact and risk stratification of balloon angioplasty for femoropopliteal disease in nitinol stenting era: Retrospective multicenter study using propensity score matching analysis
Authors: Tsuchiya Taketsugu , Takamura Takaaki , Soga Yoshimitsu , Iida Osamu , Hirano Keisuke , Suzuki Kenji , Yamaoka Terutoshi , Miyashita Yusuke , Kitayama Michihiko , Kajinami Koji 
Published: July 2016

Objective: Nitinol stenting could bring the better outcome in endovascular therapy for femoropopliteal disease. However, it might be expected that recent marked advances in both device technology and operator technique had led to improved efficacy of balloon angioplasty even in this segment. The aims of this study were to evaluate the clinical impact of balloon angioplasty for femoropopliteal disease and make risk stratification clear by propensity score matching analysis. Methods: Based on the multicenter retrospective data, 2758 patients (balloon angioplasty: 729 patients and nitinol stenting: 2029 patients), those who underwent endovascular therapy for femoropopliteal disease, were analyzed. Results: The propensity score matching procedure extracted a total of 572 cases per group, and the primary patency rate of balloon angioplasty and nitinol stenting groups after matching was significantly the same (77.2% vs 82.7% at 1 year; 62.2% vs 64.3% at 3 years; 47.8% vs 54.3% at 5 years). In multivariate Cox hazard regression analysis, significant predictors for primary patency were diabetes mellitus, regular dialysis, cilostazol use, chronic total occlusion, and intra-vascular ultra-sonography use. The strategy of balloon angioplasty was not evaluated as a significant predictor for the primary patency. After risk stratification using five items ( diabetes mellitus, regular dialysis, no use of intra-vascular ultra-sonography, chronic total occlusion, and no use of cilostazol: the DDICC score), the estimated primary patency rates of each group (low, DDICC score 0–2; moderate, DDICC score 3; high risk, DDICC score 4–5) were 88.6%, 78.3%, and 63.5% at 1 year; 75.2%, 60.7%, and 39.8% at 3 years; and 66.0%, 47.1%, and 26.3% at 5 years (p < 0.0001). The primary patency rate of balloon angioplasty and nitinol stenting groups was significantly the same in each risk stratification. Conclusion: This study suggests that balloon angioplasty does not have inferiority to nitinol stenting but does have favorable efficacy in femoropopliteal segment by careful risk stratification with the recent advance of technique.
Coagulation factors bound to procoagulant platelets concentrate in cap structures to promote clotting
Authors: Podoplelova Nadezhda A. , Sveshnikova Anastasia N. , Kotova Yana N. , Eckly Anita , Receveur Nicolas , Nechipurenko Dmitry Yu. , Obydennyi Sergey I. , Kireev Igor I. , Gachet Christian , Ataullakhanov Fazly I. , Mangin Pierre H. , Panteleev Mikhail A. 
Published: July 2016

Key PointsAll blood coagulation factors predominantly bind to a small “cap”-like region on procoagulant-activated platelets. Their concentration in this small region promotes acceleration of the membrane-dependent reactions of coagulation.
AGOUTI: improving genome assembly and annotation using transcriptome data
Authors: Zhang Simo V , Zhuo Luting , Hahn Matthew W 
Published: July 2016

Abstract

Background
Genomes sequenced using short-read, next-generation sequencing technologies can have many errors and may be fragmented into thousands of small contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. Such biases can confound inferences about the number and identity of genes within species, as well as gene gain and loss between species.

Results
We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA sequencing data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output. Running AGOUTI on both simulated and real datasets, we show that it is highly accurate and that it achieves greater accuracy and contiguity when compared with other existing methods.

Conclusion
AGOUTI is a powerful and effective scaffolder and, unlike most scaffolders, is expected to be more effective in larger genomes because of the commensurate increase in intron length. AGOUTI is able to scaffold thousands of contigs while simultaneously reducing the number of gene models by hundreds or thousands. The software is available free of charge under the MIT license.
Hydrocarbon detection for Ordovician carbonate reservoir using amplitude variation with offset and spectral decomposition
Authors: Li Yandong , Zhang Lijuan , Wang Daxing , Shi Songqun , Cui Xiaojie 
Published: July 2016

We have developed an example of hydrocarbon detection for an Ordovician cavern carbonate reservoir in western China with a burial depth exceeding 6600 m using amplitude variation with offset (AVO) and spectral decomposition. We selected six production wells, three prolific oil wells, and three brine wells to test the hydrocarbon detection method. The three oil wells have been producing for more than three years, and the three water wells only produce brine. We performed spectral decomposition to the angle gathers and analyzed amplitude variation patterns with incidence angles for different spectral components. Specifically, we compared the time corresponding to the peak spectral amplitude for different spectral components for the oil- and brine-saturated carbonate reservoirs. The main findings are as follows: (1) Oil-saturated cavern carbonate reservoirs show decreasing peak time with increasing frequency; i.e., the high-frequency components travel faster than do the low-frequency components. The maximum time difference between the 10 and 50 Hz spectral components could reach 35 ms. In contrast, the brine-saturated carbonate reservoirs do not exhibit conspicuous variation in the peak time, (2) AVO attributes extracted from the low-frequency spectral gathers are more robust than those extracted from the original seismic gathers, (3) oil-saturated cavern carbonate reservoirs cause strong energies in the low-frequency spectral components and severe attenuation to the high-frequency spectral components at large incidence angles. In contrast, the brine-saturated carbonate reservoirs do not produce such phenomenon. Rock physics analysis for carbonate reservoirs under different saturation conditions was conducted. The synthetic gathers were generated for carbonate reservoirs under oil- and brine-saturated conditions. The spectrally decomposed synthetic gathers are in agreement with the real gathers. The results indicate that AVO analysis of spectrally decomposed prestack gathers could be used as an effective hydrocarbon detection method for carbonate reservoirs.