bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of expressed CRN and RXLR effectors from two Plasmopara species causing grapevine and sunflower downy mildew
Authors: Mestre P. , Carrere S. , Gouzy J. , Piron M.‐C. , Tourvieille de Labrouhe D. , Vincourt P. , Delmotte F. , Godiard L. 
Published: October 2015

Plasmopara halstedii and Plasmopara viticola are the causative agents of downy mildew of two economically important crops, sunflower and grapevine, respectively. These phylogenetically related oomycetes are obligate biotrophs belonging to Peronosporales but have different pathological profiles. Despite the economic importance of diseases caused by both Plasmopara, genomic resources are very limited and their effector repertoire is unknown. In this study parallel transcriptome sequencing of P. halstedii and P. viticola was performed, and a Plasmopara species cDNA database (PlasmoparaSp) released containing 46 000 clusters. In oomycetes, two classes of effectors are translocated into the host cytoplasm, the RXLRs and the CRNs. The PlasmoparaSp database was screened in order to identify the repertoire of expressed effectors used by both Plasmopara species; about 50 putative RXLR and 60 CRN were identified for each. These effectors were compared within both species and with seven publicly available oomycete species representative of Peronosporales and Albuginales. Sequence analyses revealed the presence of 55 RXLR families, 12 of them shared by both Plasmopara, and 19 showing amino acid conservation with predicted peptides from at least one oomycete species. Analyses of Plasmopara spp. CRN C‐terminal variable regions revealed sequence conservation inside Plasmopara spp. and across oomycetes, with the exception of Hyaloperonospora arabidopsidis. Finally, the analyses confirmed the presence of eight CRN C‐terminal domains described in Phytophthora infestans and identified CRN effectors showing similarity to serine proteases. Species‐specific effectors were identified that may be involved in host specificity, as well as effectors conserved among oomycetes that might play important roles in the pathogen biology.
Species composition and genetic structure of Fusarium graminearum species complex populations affecting the main barley growing regions of South America
Authors: Castañares E. , Dinolfo M. I. , Del Ponte E. M. , Pan D. , Stenglein S. A. 
Published: October 2015

Members of the Fusarium graminearum species complex (FGSC), such as F. graminearum and F. asiaticum, are the main cause of fusarium head blight (FHB) of wheat and barley worldwide. In this study, 117 FGSC isolates obtained from commercial barley grain produced in Argentina (n = 43 isolates), Brazil (n = 35), and Uruguay (n = 39) were identified to species and trichothecene genotypes, and analysed using amplified fragment length polymorphism (AFLP) and sequence‐related amplified polymorphism (SRAP) markers. In addition, reductase (RED) and trichothecene 3‐O‐acetyltransferase (Tri101) were sequenced for a subset of 24 isolates. The majority of the isolates (n = 103) were identified as F. graminearum, which was the only species found in Argentina. In Uruguay, only one F. cortaderiae isolate was found among F. graminearum isolates. In Brazil, F. graminearum also dominated the collection (22/35), followed by F. meridionale (8/35), F. asiaticum (2/35), F. cortaderiae (2/35) and F. austroamericanum (1/35). Species were structured by trichothecene genotype: all F. graminearum were of the 15‐acetyldeoxynivalenol (ADON), F. meridionale, F. asiaticum and F. cortaderiae were of the nivalenol (NIV), and F. austroamericanum was of the 3‐ADON genotype. Both AFLP and SRAP data showed high levels of genetic variability, which was higher within than among countries. Isolates were not structured by country of origin. SRAP analysis grouped F. graminearum in a separate cluster from the other species within the complex. However, AFLP analysis failed to resolve the species into distinct clades with partial clustering of F. meridionale, F. austroamericanum, F. asiaticum and F. graminearum isolates.
Effect of Problem‐Solving Therapy on Depressed Low‐Income Homebound Older Adults' Death/Suicidal Ideation and Hopelessness
Authors: Choi Namkee G. , Marti C. Nathan , Conwell Yeates 
Published: October 2015

Previous study findings of psychotherapy's effect on suicide prevention have been inconsistent. This study reports the results of secondary analyses of outcome data from a short‐term depression treatment on reducing death/suicidal ideation among 158 low‐income homebound adults aged 50+. The treatment, in‐person or telehealth problem‐solving therapy (PST), compared with telephone support call, has been found effective in reducing depressive symptoms and disability among participants. Compared with support call participants, tele‐PST participants, but not in‐person PST participants, exhibited lower ideation ratings across the follow‐up period. Effect sizes at 36 weeks were 0.31 for tele‐PST and 0.17 for in‐person PST. Hopelessness mediated the effect of tele‐PST but not in‐person PST; however, in‐person PST also alleviated hopelessness, which led to lower ideation. Clinical implications of the findings are discussed.
Effect of ADAMTS13 activity turnaround time on plasma utilization for suspected thrombotic thrombocytopenic purpura
Authors: Connell Nathan T. , Cheves Tracey , Sweeney Joseph D. 
Published: October 2015

BACKGROUNDThrombotic thrombocytopenic purpura (TTP) due to deficiency of the von Willebrand‐cleaving protease ADAMTS13 is a hematologic emergency that requires prompt initiation of therapeutic plasma exchange (TPE). Long turnaround times (TATs) have precluded the use of pre‐TPE measurement of ADAMTS13 activity for the initial diagnosis in most institutions.STUDY DESIGN AND METHODSAn in‐house rapid TAT (r‐TAT) assay for ADAMTS13 activity was implemented after 18 months of validation. In a quasi‐experimental design using interrupted time series analysis, patterns of plasma utilization in patients with suspected TTP were assessed after implementation of this assay for ADAMTS13 activity and compared to utilization patterns for patients who received plasma exchange before r‐TAT assay implementation designated the standard TAT period.RESULTSIn the 18 months after implementation of the r‐TAT ADAMTS13 assay, there was a significant reduction in plasma utilization per patient suspected of having TTP (mean, 144.5 units vs. 63.3 units of plasma per patients suspected of having TTP; p = 0.002). The mean number of exchanges per patient and mean number of exchanges after achieving a platelet count of at least 150 × 109/L were lower in the r‐TAT cohort (p < 0.001 for both). There was no significant difference in 30‐day mortality.CONCLUSIONSImplementation of a rapid turnaround assay for ADAMTS13 resulted in a significant reduction in plasma utilization for patients with suspected TTP, without an increase in mortality. This study demonstrates that these data, provided in a timely fashion, can avoid unnecessary plasma exchange in patients who do not have TTP.
Glucose‐6‐phosphate dehydrogenase activity decreases during storage of leukoreduced red blood cells
Authors: Peters Anna L. , van Bruggen Robin , de Korte Dirk , Van Noorden Cornelis J.F. , Vlaar Alexander P.J. 
Published: October 2015

BACKGROUNDDuring storage, the activity of the red blood cell (RBC) antioxidant system decreases. Glucose‐6‐phosphate dehydrogenase (G6PD) is essential for protection against oxidative stress by producing NADPH. G6PD function of RBC transfusion products is reported to remain stable during storage, but activity was measured in hemolysates and not in individual RBCs. We hypothesized that analysis of G6PD activity in individual RBC identifies storage‐dependent changes in G6PD function.STUDY DESIGN AND METHODSSeven units of stored leukoreduced RBCs, stored in saline‐adenine‐glucose‐mannitol, were sampled every week up to 6 weeks of storage. G6PD activity was determined with the cytofluorometric method and expressed as mean fluorescent intensity (MFI) per RBC.RESULTSDuring storage, G6PD activity decreased significantly. Mean MFI after 3 days of storage was 27.8 ± 8.8 and gradually decreased significantly to 18.0 ± 8.3 after 42 days.CONCLUSIONG6PD activity decreases during storage of leukoreduced RBCs. Our results may form a new target to improve storage conditions of RBCs and subsequently improve the quality of transfusion products.
Can the interval between antibody identifications be increased for alloimmunized patients?
Authors: Goss Cheryl , Avecilla Scott T. , Garbaini Jennifer , Degtyaryova Diana , Lo Dian , Chang Dustin Y.M. , Cushing Melissa 
Published: October 2015

BACKGROUNDNew alloantibody formation is unpredictable in patients who have been previously alloimmunized. Pretransfusion testing is designed to detect these antibodies while antibody identification (ABI) techniques are designed to identify the specificity of the antibody. Pretransfusion testing intervals are prescribed by regulatory and accrediting agencies, intervals for ABI in alloimmunized patients are not. Our institution evaluated the safety of increasing the interval from every 72 hours to 14 days. The current 72‐hour interval was chosen at our institution to align with AABB Standard 5.14.3.2, which requires a pretransfusion specimen drawn within 3 days of the scheduled transfusion for potentially immunized patients.STUDY DESIGN AND METHODSOver 2 years, all ABI entries in the laboratory information system were screened. All cases of alloimmunized patients with an additional antibody specificity that developed within 14 days of a previous ABI were reviewed and confirmed by four transfusion medicine physicians.RESULTSInitially, 8948 entries were screened. Thirty patients were identified to have formed 33 newly identified clinically significant alloantibodies within 14 days. After further categorization, only 13 antibodies (0.15% of all ABIs, 0.47% of alloimmunized patients examined) were deemed to be newly formed clinically significant antibodies that would have led to a change in transfusion practice.CONCLUSIONRetrospective analysis of ABI results over a 2‐year period revealed that 0.47% of previously alloimmunized patients that have samples for pretransfusion testing develop a new clinically significant alloantibody in 14 days or less. While there would be significant resource advantages to increasing the duration between repeat ABI, it does not outweigh the risk of a potential hemolytic transfusion reaction.
The Effectiveness of Manual Lymphatic Drainage in Patients With Orthopedic Injuries
Authors: Majewski-Schrage Tricia , Snyder Kelli 
Published: October 2015

Clinical Scenario:Managing edema after trauma or injury is a primary concern for health care professionals, as it is theorized that delaying the removal of edema will increase secondary injury and result in a longer recovery period. The inflammatory process generates a series of events, starting with bleeding and ultimately leading to fluid accumulation in intercellular spaces and the formation of edema. Once edema is formed, the lymphatic system plays a tremendous role in removing excess interstitial fluid and returning the fluid to the circulatory system. Therefore, rehabilitation specialists ought to use therapies that enhance the uptake of edema via the lymphatic system to manage edema; however, the modalities commonly used are ice, compression, and elevation. Modalities such as these may be effective at preventing swelling but present limited evidence to suggest that the function of the lymphatic system is enhanced. Manual lymphatic drainage (MLD) is a manual therapy technique that assists the lymphatic system function by promoting variations in interstitial pressures by applying light pressure using different hand movements.Focused Clinical Question:Does MLD improve patient- and disease-oriented outcomes for patients with orthopedic injuries?
An Exertional Heat Stroke Survivor’s Return to Running: An Integrated Approach on Treatment, Recovery, and Return to Activity
Authors: Adams William M. , Hosokawa Yuri , Huggins Robert A. , Mazerolle Stephanie M. , Casa Douglas J. 
Published: October 2015

Context:Evidence-based best practices for the recognition and treatment of exertional heat stroke (EHS) indicate that rectal thermometry and immediate, aggressive cooling via cold-water immersion ensure survival from this medical condition. However, little is known about the recovery, medical follow-up, and return to activity after an athlete has suffered EHS.Objective:To highlight the transfer of evidenced-based research into clinical practice by chronicling the treatment, recovery, and return to activity of a runner who suffered an EHS during a warm-weather road race.Design:Case study.Setting:Warm-weather road race.Participant:53-y-old recreationally active man.Intervention:A runner’s treatment, recovery, and return to activity from EHS and 2014 Falmouth Road Race performance.Main Outcomes:Runner’s perceptions and experiences with EHS, body temperature, heart rate, hydration status, exercise intensity.Results:The runner successfully completed the 2014 Falmouth Road Race without incident of EHS. Four dominant themes emerged from the data: predisposing factors, ideal treatment, lack of medical follow-up, and patient education. The first theme identified 3 predisposing factors that contributed to the runner’s EHS: hydration, sleep loss, and lack of heat acclimatization. The runner received ideal treatment using evidence-based best practices. A lack of long-term medical care following the EHS with no guidance on the runner’s return to full activity was observed. The runner knew very little about EHS before the 2013 race, which drove him to seek knowledge as to why he suffered EHS. Using this newly learned information, he successfully completed the 2014 Falmouth Road Race without incident.Conclusions:This case supports prior literature examining the factors that predispose individuals to EHS. Although evidence-based best practices regarding prompt recognition and treatment of EHS ensure survival, this case highlights the lack of medical follow-up and physician-guided return to activity after EHS.
Should Cooling Vests Be Used to Treat Exertional Heatstroke? A Critically Appraised Topic
Authors: Keen Megan L. , Miller Kevin C. 
Published: October 2015

Clinical Scenario:Exercise performed in hot and humid environments increases core body temperature (TC). If TC exceeds 40.5°C for prolonged periods of time, exertional heat stroke (EHS) may occur. EHS is a leading cause of sudden death in athletes. Mortality and morbidity increase the longer the patient’s TC remains above 40.5°C; thus, it is imperative to initiate cooling as quickly as possible. Acceptable cooling rates in EHS situations are 0.08–0.15°C/min, while ideal cooling rates are above 0.16°C/min. Cooling vests are popular alternatives for cooling hyperthermic adults. Most vests cover the anterior and posterior torso and have varying numbers of pouches for phase-change materials (eg, gel packs); some vests only use circulating water to cool. While cooling vests offer several advantages (eg, portability), studies demonstrating their effectiveness at rapidly reducing TC in EHS scenarios are limited.Clinical Question:Are TC cooling rates acceptable (ie, >0.08°C/min) when hyperthermic humans are treated with cooling vests postexercise?Summary of Findings:No significant differences in TC cooling rates occurred between cooling vests and no cooling vests. Cooling rates across all studies were ≤0.053°C/min.Clinical Bottom Line:Cooling vests do not provide acceptable cooling rates of hyperthermic humans postexercise and should not be used to treat EHS. Instead, EHS patients should be treated with cold-water immersion within 30 min of collapse to avoid central nervous system dysfunction and organ failure.Strength of Recommendation:Strong evidence (eg, level 2 studies with PEDro scores ≥5) suggests that cooling vests do not reduce TC quickly and thus should not be used in EHS scenarios.
Hip Rotations’ Influence of Electromyographic Activity of Gluteus Medius Muscle During Pelvic-Drop Exercise
Authors: Monteiro Renan Lima , Facchini Joana Hoverter , de Freitas Diego Galace , Callegari Bianca , João Sílvia Maria Amado 
Published: October 2015

Context:Pelvic-drop exercises are often used to strengthen the gluteus medius (GM) muscle with the aim of increasing or prioritizing its recruitment. However, the effect of hip rotation on the performance of the action of the GM is unknown.Objective:To evaluate the effect of hip rotation on the recruitment of the GM, tensor fasciae latae (TFL), and quadratus lumborum (QL).Method:Seventeen healthy subjects performed 2 sets of 4 repetitions of pelvic-drop exercise in random order with pelvic-drop lateral, medial, and neutral rotation of the hip.Main Outcome Measures:The electromyographic (EMG) activity of the GM, TFL, and QL was evaluated using surface electromyography.Results:There were significant increases in the activation of the GM with medial and neutral rotation compared with lateral rotation (P = .03, P = .01, respectively), and there was no difference between medial and neutral rotation (P = 1.00). There was no difference in EMG activity of the TFL and QL in any of the positions. The GM:TFL ratio was the same in all analyzed positions. Regarding the GM:QL ratio, there was a significant increase with medial rotation compared with lateral rotation (P = .02).Conclusions:Pelvic-drop exercises are more efficient for activating the GM when the hip is in medial rotation and neutral position.
On modules with cyclic socle
Authors: Assem Ali 
Published: October 2015

The extension problem for linear codes over modules with respect to Hamming weight was already settled in [J. A. Wood, Code equivalence characterizes finite Frobenius rings, Proc. Amer. Math. Soc. 136 (2008) 699–706; Foundations of linear codes defined over finite modules: The extension theorem and MacWilliams identities, in Codes Over Rings, Series on Coding Theory and Cryptology, Vol. 6 (World Scientific, Singapore, 2009), pp. 124–190]. A similar problem arises naturally with respect to symmetrized weight compositions (SWC). In 2009, Wood proved that Frobenius bimodules have the extension property (EP) for SWC. More generally, in [N. ElGarem, N. Megahed and J. A. Wood, The extension theorem with respect to symmetrized weight compositions, in 4th Int. Castle Meeting on Coding Theory and Applications (2014)], it is shown that having a cyclic socle is sufficient for satisfying the property, while the necessity remained an open question. Here, landing in midway, a partial converse is proved. For a (not small) class of finite module alphabets, the cyclic socle is shown necessary to satisfy the EP. The idea is bridging to the case of Hamming weight through a new weight function. Note: All rings are finite with unity, and all modules are finite too. This may be re-emphasized in some statements. The convention for left homomorphisms is that inputs are to the left.
Detecting differentially expressed genes by smoothing effect of gene length on variance estimation
Authors: Tang Jinyang , Wang Fei 
Published: October 2015

Next-generation sequencing technologies are widely used in genome research, and RNA sequencing (RNA-Seq) is becoming the main application for gene expression profiling. A large number of computational methods have been developed for analyzing differentially expressed (DE) genes in RNA-Seq data. However, most existing algorithms prefer to call long genes as DE. Short DE genes are rarely detected. In this work, we set out to gain insight into the influence of gene length on RNA-Seq data analysis and to figure out the effect of gene length on variance estimation of RNA-Seq read counts, which is important for statistic test to identify DE genes. We proposed a balanced method of hunting for short DE genes with significance by smoothing a gene length factor. Computational experiments indicate that our method performs well. Software available: http://www.iipl.fudan.edu.cn/lenseq/ .
Diffusion-weighted imaging in oral squamous cell carcinoma using 3 Tesla MRI: is there a chance for preoperative discrimination between benign and malignant lymph nodes in daily clinical routine?
Authors: Wendl Christina M , Müller Steffen , Eiglsperger Johannes , Fellner Claudia , Jung Ernst M , Meier Johannes K 
Published: October 2015

Background Preoperative staging of cervical lymph nodes is important to determine the extent of neck dissection in patients with oral squamous cell carcinoma (OSCC). Purpose To evaluate whether a preoperative discrimination of benign and malignant cervical lymph nodes with diffusion-weighted imaging (DWI) (3T) is feasible for clinical application. Material and Methods Forty-five patients with histological proven OSCC underwent preoperative 3T-MRI. DWI (b = 0, 500, and 1000 s/mm2) was added to the standard magnetic resonance imaging (MRI) protocol. Mean apparent diffusion coefficients (ADCmean) were measured for lymph nodes with 3 mm or more in short axis by two independent readers. Finally, these results were matched with histology. Results Mean ADC was significantly higher for malignant than for benign nodes (1.143 ± 0.188 * 10−3 mm2/s vs. 0.987 ± 0.215 * 10−3 mm2/s). Using an ADC value of 0.994 * 10−3 mm2/s as threshold results in a sensitivity of 80%, specificity of 65%, positive predictive value of 31%, and negative predictive value of 93%. Conclusion Due to a limited sensitivity and specificity DWI alone is not suitable to reliably discriminate benign from malignant cervical lymph nodes in daily clinical routine. Hence, the preoperative determination of the extent of neck dissection on the basis of ADC measurements is not meaningful.
Materials characterization of explanted polypropylene hernia mesh: Patient factor correlation
Authors: Smith Sarah E , Cozad Matthew J , Grant David A , Ramshaw Bruce J , Grant Sheila A 
Published: October 2015

This study quantitatively assessed polypropylene (PP) hernia mesh degradation and its correlation with patient factors including body mass index, tobacco use, and diabetes status with the goal of improving hernia repair outcomes through patient-matched mesh. Thirty PP hernia mesh explants were subjected to a tissue removal process followed by assessment of their in vivo degradation using Fourier transform infrared, differential scanning calorimetry, and thermogravimetric analysis analyses. Results were then analyzed with respect to patient factors (body mass index, tobacco use, and diabetes status) to determine their influence on in vivo hernia mesh oxidation and degradation. Twenty of the explants show significant surface oxidation. Tobacco use exhibits a positive correlation with modulated differential scanning calorimetry melt temperature and exhibits significantly lower TGA decomposition temperatures than non-/past users. Chemical and thermal characterization of the explanted meshes indicate measurable degradation while in vivo regardless of the patient population; however, tobacco use is correlated with less oxidation and degradation of the polymeric mesh possibly due to a reduced inflammatory response.