bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the binding loops configuration and surface adaptation of different crystallized single‐domain antibodies in response to various antigens
Authors: Al Qaraghuli Mohammed M. , Ferro Valerie A. 
Published: November 2016

AbstractMonoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single‐domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full‐length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes.
Stochastic finite integration technique for magnetostatic problems
Authors: Codecasa Lorenzo , Di Rienzo Luca 
Published: November 2016

AbstractBoth nonintrusive and intrusive stochastic approaches on the basis of polynomial chaos expansion are presented for the finite integration technique over generic polyhedral grids for 3D magnetostatic linear problems. Such algorithms outperform Monte Carlo methods (when the number of random parameters is small), both in accuracy and efficiency. A novel algorithm for the intrusive approach is also provided, by which the intrusive approach becomes less computationally expensive than the nonintrusive approach. Validation is performed by solving a magnetic circuit where the reluctivity is uncertain.
Assessment of future ENSO changes in a CMIP3/CMIP5 multi‐model and multi‐index framework
Authors: Keupp Luzia , Pollinger Felix , Paeth Heiko 
Published: November 2016

ABSTRACTAs main mode of interannual climate variability with worldwide teleconnections, El Niño‐Southern Oscillation (ENSO) holds high ecological, economical and social relevance. So far, studies on future ENSO changes draw a rather incoherent picture across climate models and ENSO indices. Here, we assess climate change signals and respective uncertainties in the frequency and variance of ENSO events using a comprehensive multidimensional approach: 10 different ENSO indices based on five climate variables and derived from four CMIP3 and nine CMIP5 models are investigated and compared systematically. Finally, one dimension of the problem (of various indices and various models as well as realizations) is removed by combining the 10 ENSO indices to a single ‘super’‐index, defined in the Empirical Orthogonal Function space.The most common signal across models and indices is found to be an increase of year‐to‐year variability of ENSO events until the end of our century, especially in the combined index. A significant strengthening in frequency occurs only in terms of La Niña events in some indices, whereas El Niño events appear to be barely sensitive to radiative forcing during the 21st century. This study highlights the importance of taking a more holistic multi‐model and multi‐index viewpoint when assessing future changes in ENSO behaviour and addressing higher‐moment characteristics of ENSO.
Influence of growing altitude, shade and harvest period on quality and biochemical composition of Ethiopian specialty coffee
Authors: Tolessa Kassaye , D'heer Jolien , Duchateau Luc , Boeckx Pascal 
Published: November 2016

AbstractBACKGROUNDCoffee quality is a key characteristic for the international market, comprising cup quality and chemical bean constituents. In Ethiopia, using total specialty cup scores, coffees are grouped into Q1 (specialty 1) ≥ 85 and Q2 (80–84.75). This classification results in market segmentation and higher prices. Although different studies have evaluated the effects of altitude and shade on bean quality, optimum shade levels along different altitudinal ranges are not clearly indicated. Information on effects of harvest periods on coffee quality is also scanty. The present study examined the influences of these factors and their interactions on Ethiopian coffee qualityRESULTSCoffee from high altitude with open or medium shade and early to middle harvest periods had a superior bean quality. These growing conditions also favoured the production of beans with lower caffeine. An increasing altitude, from mid to high, at approximately 400 m, decreased caffeine content by 10%. At high altitude, dense shade decreased Q1 coffee by 50%. Compared to late harvesting, early harvesting increased the percentage from 27% to 73%. At mid altitude, > 80% is Q2 coffee.CONCLUSIONSChanges of quality scores driven by altitude, shade and harvest period are small, although they may induce dramatic switches in the fraction Q1 versus Q2 coffee. The latter affects both farmers' profits and competitiveness in international markets. © 2016 Society of Chemical Industry
Increasing meat product functionality by the addition of milled flaxseed Linum usitatissimum
Authors: Zając Marzena , Kulawik Piotr , Tkaczewska Joanna , Migdał Władysław , Pustkowiak Henryk 
Published: November 2016

AbstractBACKGROUNDFunctional meat products are still rare on the market because it is difficult to incorporate new ingredients and obtain both a healthy and acceptable product. Flaxseed is known for its beneficial properties and, in the present study, it was used as an ingredient in the production of homogenised and liver sausages (0%, 5% and 10% flaxseed addition).RESULTSHomogenised and liver sausages with the addition of 5% flaxseed were given the highest scores by the consumers, although the colour changed with the addition of flaxseed. The spreadability and hardness of the liver sausages increased with the addition of flaxseed, whereas the texture of homogenised sausages did not change. Addition of flaxseed improved the fatty acids profile from a health point of view for both products, as a result of increasing n‐3 fatty acids and overall polyunsaturated fatty acids content. Values for thiobarbituric acid reactive substances were higher in products with flaxseed and were observed to increase during storage.CONCLUSIONThe results of the present study indicate that it is possible to obtain products that are acceptable by consumers and, at the same time, are more healthy. A high level of α‐linolenic acid in the sausages at a level of addition of 5% allows the product to be labelled with information regarding their high omega‐3 fatty acid content. However, those products are more susceptible to oxidation. © 2016 Society of Chemical Industry
Quality of life before and after different treatment modalities in peripheral facial palsy: A systematic review
Authors: Luijmes Robin E. , Pouwels Sjaak , Beurskens Carien H. G. , Kleiss Ingrid J. , Siemann Ietske , Ingels Koen J. A. O. 
Published: November 2016

ObjectivesA systematic review was conducted to investigate the effect of peripheral facial palsy (PFP) on the quality of life (QoL). Secondly, we investigated if different treatment modalities influence the QoL of patients with PFP.MethodsA multidatabase systematic literature search was performed using the following databases: PubMed, Embase, MEDLINE, and The Cochrane Library from the earliest date of each database up to August 2015. The inclusion criteria were either prospective and/or retrospective cohort trials and/or case series measurement of QoL before and after treatment, patients with PFP (irrespective of etiology), and various treatment modalities (medication, physical therapy, botulinum toxin injections, and several types of surgical procedures). Two authors rated the methodological quality of the included studies independently using the Newcastle–Ottawa Quality Assessment Scale for nonrandomized studies.ResultsTwo hundred fifty‐eight studies were found, of which 14 studies met the inclusion criteria. Most studies were assessed to be of fair to good methodological quality. The Cohen's κ (between author r.e.l. and s.p.) was 0.68. Eight different questionnaires were used to measure QoL, of which the Facial Clinimetric Evaluation scale was used most frequent. After different modalities, all studies showed significant improvements in terms of QoL.ConclusionsThis study found significant improvement when measuring QoL before and after different treatment modalities in patients with peripheral facial palsy. Future research should focus on patients with PFP due to the same etiology and use of valid QoL instruments for outcome measures. Laryngoscope, 127:1044–1051, 2017
Potassium titanyl phosphate laser welding following complete nerve transection
Authors: Bhatt Neel K. , Mejias Christopher , Kallogjeri Dorina , Gale Derrick C. , Park Andrea M. , Paniello Randal C. 
Published: November 2016

Objectives/HypothesisCranial nerve transection during head and neck surgery is conventionally repaired by microsuture reanastomosis. Laser nerve welding (LNW), using CO2 laser to spot‐weld the epineurium of transected nerve endings, has been shown in animal models to be a novel alternative to microsuture repair. This method avoids needle/suture material and minimizes instrumentation of the nerve. We hypothesized that potassium titanyl phosphate (KTP) laser would be superior to CO2 laser in repairing transected nerves. Using a rat posterior tibial nerve injury model, we compared CO2 laser, KTP laser, and microsuture reanastomosis.Study DesignAnimal study.MethodsAnimals underwent unilateral posterior tibial nerve transection. The injury was repaired by microsuture repair (n = 15), CO2 laser repair (n = 15), or KTP laser repair (n = 15). Weekly walking tracks were performed to measure functional recovery. Nerve segments were harvested for axon counting.ResultsAt 6 weeks, the KTP LNW had the best functional recovery (92.4 ± 8.6%) compared to microsuture repair (84.5 ± 10.2%, difference 7.9%, 95% confidence interval [CI]: 0.84%‐14.96%). CO2 laser repair had a functional recovery of 86.8 ± 11.2%. KTP LNW had better axon recovery compared to transection/repair (difference 530.7 axons, 95% CI: 329.9‐731.5). Operative time for the microsuture repair was 18.2 ± 6.8 minutes, compared to 5.8 ± 3.7 minutes for the LNW groups (difference 12.4 minutes, 95% CI: 8.6‐16.2 minutes).ConclusionsKTP, CO2, and microsuture repair all showed good functional recovery following complete transection of the posterior tibial nerve. Following complete nerve transection during head and neck surgery, KTP LNW may be a novel alternative to microsuture repair.Level of EvidenceNA Laryngoscope, 127:1525–1530, 2017
Chronic parotitis with multiple calcifications: Clinical and sialendoscopic findings
Authors: Jáuregui Emmanuel , Kiringoda Ruwan , Ryan William R. , Eisele David W. , Chang Jolie L. 
Published: November 2016

Objectives/HypothesisTo characterize clinical, imaging, and sialendoscopy findings in patients with chronic parotitis and multiple parotid calcifications.Study DesignRetrospective review.MethodsClinical history, radiographic images and reports, lab tests, and operative reports were reviewed for adult patients with chronic parotitis and multiple parotid calcifications who underwent parotid sialendoscopy.ResultsThirteen of 133 (10%) patients undergoing parotid sialendoscopy for chronic sialadenitis had more than one calcification in the region of the parotid gland. Seven patients (54%) were diagnosed with immune‐mediated disease from autoimmune parotitis (positive Sjögren's antibodies or antinuclear antibodies) or human immunodeficiency virus (HIV) disease. The six patients (46%) who did not have an immune‐mediated disorder had most calcifications located anterior or along the masseter muscle. Eight of 13 patients (61%) had at least one calculus found in the parotid duct on sialendoscopy. Four patients (38%) had multiple punctate calcifications within the parotid gland, all of whom had either autoimmune parotitis or HIV. None of the proximal or punctate parotid calcifications posterior to the masseter were visualized on sialendoscopy.ConclusionsChronic parotitis in conjunction with multiple parotid calcifications is uncommon and was identified in 10% of our cohort. We contrast two classifications of parotid calcifications: 1) intraductal stones that cause recurrent duct obstruction and are often located within the main parotid duct along or anterior to the masseter and 2) punctate intraparenchymal parotid gland calcifications that are not visualized on sialendoscopy and may represent underlying inflammatory disease.Level of Evidence4 Laryngoscope, 127:1565–1570, 2017
Prevalence of polyp recurrence after endoscopic sinus surgery for chronic rhinosinusitis with nasal polyposis
Authors: DeConde Adam S. , Mace Jess C. , Levy Joshua M. , Rudmik Luke , Alt Jeremiah A. , Smith Timothy L. 
Published: November 2016

Objectives/HypothesisChronic rhinosinusitis with nasal polyposis (CRSwNP) is a disease process that is driven, in part, by intrinsic mucosal inflammation. Surgery plus continued medical therapy is commonly elected by medically recalcitrant, symptomatic patients. The objective was to evaluate the prevalence of nasal polyp recurrence up to 18 months after endoscopic sinus surgery (ESS) with congruent continuing medical management.Study DesignProspective, multicenter cohort of adult patients undergoing ESS for medically recalcitrant CRSwNP performed between August 2004 and February 2015.MethodsAll patients received baseline nasal endoscopy quantified using Lund‐Kennedy grading. All patients included for final analysis provided at least 6 months of postoperative endoscopy examinations. Multivariate analysis was used to identify risk factors for polyp recurrence.ResultsThree hundred sixty‐three CRSwNP patients having undergone ESS involving polypectomy were enrolled. A total of 244 (67%) participants had graded postoperative endoscopies with average of follow‐up of 14.3 ± 7.0 months. Surgery plus postoperative medical management significantly improved endoscopy total scores at 6 months (P < .001). The recurrence of nasal polyposis 6 months after ESS was 35% (68/197), compared to 38% (48/125) after 12 months, and 40% (52/129) after 18 months. Multivariate analysis identified both prior ESS (odds ratio [OR]: 2.6, 95% confidence interval [CI]: 1.5‐4.6; P = .001) and worse preoperative polyposis severity (OR: 1.4, 95% CI: 1.1‐1.8; P = .016) as risk factors for recurrent polyposis.ConclusionsPolyp recurrence is common after ESS with control of polyps up to 18 months found in approximately 60% to 70% of patients. Investigation into both surgical and medical management strategies is warranted to improve upon the observed prevalence of recurrence.Level of Evidence2c. Laryngoscope, 127:550–555, 2017
TGF‐β antagonist attenuates fibrosis but not luminal narrowing in experimental tracheal stenosis
Authors: Antón‐Pacheco Juan L. , Usategui Alicia , Martínez Iván , García‐Herrero Carmen M. , Gamez Antonio P. , Grau Montserrat , Martínez Ana M. , Rodríguez‐Peralto José L. , Pablos José L. 
Published: November 2016

ObjectiveAcquired tracheal stenosis (ATS) is an unusual disease often secondary to prolonged mechanical trauma. Acquired tracheal stenosis pathogenesis involves inflammation and subsequent fibrosis with narrowing of the tracheal lumen. Transforming growth factor‐β1 (TGF‐β) represents a pivotal factor in most fibrotic processes, and therefore a potential target in this context. The aim of this study is to analyze the role of TGF‐β as a target for anti‐fibrotic interventions in tracheal stenosis.MethodsHuman stenotic tracheobronchial tissues from patients with benign airway stenosis and normal controls from pneumonectomy specimens were analyzed. Tracheal stenosis was induced in adult NZ rabbits by a circumferential thermal injury to the mucosa during open surgery and re‐anastomosis. Rabbits were treated postoperatively with a peritracheal collagen sponge containing a TGF‐β peptide antagonist (p17) or vehicle. Fibrosis was determined by Masson's trichrome staining, and smooth muscle cell α‐actin+ (α‐SMA+ Confirm accuracy.) myofibroblasts, connective tissue growth factor (CTGF), and p‐Smad2/3 expression by immunohistochemistry.ResultsHuman and rabbit stenotic tissues showed extensive submucosal fibrosis, characterized by significantly increased α‐SMA+ myofibroblasts and CTGF expression. In human stenotic lesions, increased p‐Smad2/3+ nuclei were also observed. p17 treatment significantly reduced the fibrotic thickness, as well as the density of α‐SMA+ myofibroblasts and CTGF+ cells in rabbit stenotic lesions, but failed to improve the luminal area.ConclusionATS is characterized by a TGF‐β dependent fibrotic process, but reduction of the fibrotic component by TGF‐β1 antagonist therapy was not sufficient to improve tracheal narrowing, suggesting that fibrosis may not be the main contributor to luminal stenosis.Level of EvidenceNA. Laryngoscope, 127:561–567, 2017
Does treatment of paradoxical vocal fold movement disorder decrease asthma medication use?
Authors: Kramer Scott , deSilva Brad , Forrest L. Arick , Matrka Laura 
Published: November 2016

Objectives/HypothesisTo determine whether diagnosis and treatment of paradoxical vocal fold movement disorder (PVFMD) leads to decreased asthma medication use. Secondary objectives include determining initial rate of asthma medication use, characterizing symptom improvement, and correlating with pulmonary function testing (PFT).Study DesignProspective observational study.MethodsPatients newly diagnosed with PVFMD at a single institution were recruited to participate. Medication questionnaires were completed at the initial visit, at the first return visit for therapy, and at 6 months. PFTs were reviewed when available.ResultsSixty‐six patients were recruited; the study was closed early because findings reached significance. Fifty‐six patients (85%) were taking asthma medication at presentation. Forty‐four patients presented with PFTs, and two‐thirds were normal. Forty‐two patients completed follow‐up questionnaires; 79% decreased asthma medication use (P < .001), and 82% reported symptom improvement. Seventy‐seven percent of patients participated in therapy and 23% did not, with equal rates of decrease in asthma medication use between these groups. Outcomes did not vary based on PFT pattern (i.e., obstructive vs. nonobstructive, P = .75).ConclusionsDiagnosis and treatment of PVFMD lead to a decline in asthma medication use. This decrease occurred alongside symptom improvement and irrespective of PFT findings. Use of asthma medication in this patient population is high, at 85%.Level of Evidence4. Laryngoscope, 127:1531–1537, 2017
Sedimentary oxygen dynamics in a seasonally hypoxic basin
Authors: Seitaj Dorina , Sulu‐Gambari Fatimah , Burdorf Laurine D. W. , Romero‐Ramirez Alicia , Maire Olivier , Malkin Sairah Y. , Slomp Caroline P. , Meysman Filip J. R. 
Published: November 2016

AbstractSeasonal hypoxia refers to the oxygen depletion that occurs in summer in the bottom water of stratified systems, and is increasingly observed in coastal areas worldwide. The process induces a seasonal cycle on the biogeochemistry of the underlying sediments, which remains poorly quantified. Here, we investigated the sedimentary oxygen consumption within Lake Grevelingen (The Netherlands), a saline coastal reservoir that is impacted by yearly recurrent bottom water hypoxia. Monthly sampling campaigns were conducted throughout 2012 at three sites along a depth gradient. Macrofauna sampling and sediment profile imaging demonstrated how summer hypoxia strongly impacts the benthic communities below 15 m of water depth. Benthic fluxes of oxygen, dissolved inorganic carbon, total alkalinity, and ammonium were determined by closed core incubations, while oxygen depth profiles were recorded by microsensor profiling of sediment cores. Our results reveal a pronounced seasonality in the sedimentary oxygen consumption. Low uptake rates in summer were caused by oxygen limitation, and resulted in the build‐up of an “oxygen debt” through the accumulation of reduced iron sulfides. Highest oxygen uptake rates were recorded in fall, linked to the reoxidation of the pool of iron sulfides in the top layer. However, uptake rates remained unexpectedly high during winter and early spring, likely associated with the oxidation of iron sulfides down to centimeters depth due to the electrogenic sulfur oxidation by cable bacteria. Overall, our results suggest that the sedimentary oxygen dynamic in seasonally hypoxic coastal systems is characterized by a strongly amplified “oxygen debt” dynamics induced by cable bacteria.
Reconstructing the seasonal dynamics and relative contribution of the major processes sustaining CO2 emissions in northern lakes
Authors: Vachon Dominic , Solomon Christopher T. , del Giorgio Paul A. 
Published: November 2016

AbstractLake CO2 emissions are an important component of the carbon balance of northern landscapes, yet the temporal dynamics of the underlying mechanisms sustaining CO2 emissions are less understood. Here, we reconstruct the major biotic and abiotic processes influencing CO2 dynamics over an annual cycle in three limnologically different lakes, using a combination of empirical measurements and process‐based modeling. Our results suggest that the relative importance of each process sustaining CO2 emissions is not only variable among lakes, but also highly variable among seasons within one lake. Spring CO2 emissions were largely sustained by the release of under ice accumulation (between about 50–100%), although photo‐chemical DOC mineralization and hydrologic CO2 loading were also relatively important. In summer, due to warmer temperature, pelagic and benthic metabolism were the main sources of CO2 emissions. In the fall, lake CO2 emissions were generally sustained by hydrologic CO2 inputs, while hypolimnetic CO2 accumulation and release also contributed to fall CO2 emission in the deepest lake. On an annual basis, lake CO2 emissions ranged between 21.4 g C m−2 yr−1 and 55.5 g C m−2 yr−1. Our results confirm that the major processes all contributed significantly to CO2 emissions, but their relative contributions were modulated by the seasonal patterns in climate and hydrology, and by differences in morphology and organic carbon inputs among lakes. These lake‐ and season‐specific features need to be considered both in the upscaling of lake processes at regional scales, and in predicting lake CO2 emissions under scenarios of climate and environmental change.