bluuebunny/crossref_metadata_2025 huggingface dataset:
Physicochemical Characteristics of Fungal Xylanases and their Potential for Biobleaching of Kraft and Non-wood Pulps
Authors: Kmetzki Ana C. F. , Henn Caroline , Moraes Sandra S. , Silva Nyéssia F. S. , Kadowaki Marina K.
Published: February 2020

Xylanases are enzymes with a wide variety of biotechnological applications, such as in the bioconversion of lignocellulosic materials, improvement of feed digestibility, and bleaching kraft pulps to increase pulp brightness. Many studies have been conducted and published over the years on cellulose pulp bleaching due to the need to search for more sustainable tools and thus reduce environmental pollution. Thus, in this review, we focus on analyzing the biochemical properties of xylanases produced by mesophilic and thermophilic fungi that have been used in the bleaching processes of kraft and non-wood pulps. Eucalyptus kraft pulp is still one of the most used raw materials in the production of pulp and paper, while straw and bagasse are alternative sources of non-wood pulps. Thermophilic fungal xylanases show optimum enzymatic activity at high temperatures and a shorter treatment period when compared to mesophilic xylanases in the bleaching step. However, mesophilic fungal xylanases exhibit a longer period of enzymatic treatment but achieve a satisfactory brightness and kappa number. Hence, these approaches will contribute to future applications of these xylanolytic enzymes in pulp and paper industries.
European Brown hare (Lepus europaeus) as a source of emerging and re‐emerging pathogens of Public Health importance: A review
Authors: Tsokana Constantina N. , Sokos Christos , Giannakopoulos Alexios , Birtsas Periklis , Valiakos George , Spyrou Vassiliki , Athanasiou Labrini V. , Rodi Burriel Angeliki , Billinis Charalambos
Published: February 2020

European brown hare (Lepus europaeus, EBH) is probably the most important game animal in Europe throughout its historical distribution. The decline in its populations across its geographic range in Europe have been attributed to factors such as reproductive rate and the ability for adaptation, climate, feed availability, predators, anthropogenic factors and diseases. Apart from common diseases of hares with a high impact on their mortality such as European Brown hare Syndrome, EBH has been involved in the epidemiology of pathogens with zoonotic potential. In this work, the role of EBH as a source of Crimean–Congo haemorrhagic fever virus (CCHFV), Hepatitis E virus (HEV), Yersinia spp., Brucella spp., Francisella tularensis, Toxoplasma gondii and Leishmania infantum is discussed. Hares may significantly contribute to the epidemiology of important emerging zoonotic pathogens through maintenance of high endemicity levels as in the case of CCHFV, as a reservoir of important pathogens such as Yersinia spp., B. suis, F. tularensis and L. infantum and as a potential source of T. gondii for other animals, especially for carnivores but also for humans. However, EBH may also be a host of minor importance as in the case of HEV. The continuous surveillance of hare populations will enable the collection of information on the population health status and the pathogens currently circulating in the area posing risk for wildlife, domestic animals and humans. The possible live animal translocations of infected hares, the fact that this species acts as a host of vectors (fleas, ticks, mosquitoes and sandflies) and the prey of carnivores and omnivores that travel in great distances getting into contact with domestic animals and humans, further highlights the need to be included in surveillance studies. Besides, the hunter‐harvested EBH population is an excellent indicator for recent pathogen transmission due to its short lifespan.
Detection of the phycotoxin pectenotoxin-2 in waters around King George Island, Antarctica
Authors: Krock Bernd , Schloss Irene R. , Trefault Nicole , Tillmann Urban , Hernando Marcelo , Deregibus Dolores , Antoni Julieta , Almandoz Gastón O. , Hoppenrath Mona
Published: February 2020

In order to set a base line for the observation of planktonic community changes due to global change, protistan plankton sampling in combination with phycotoxin measurements and solid phase adsorption toxin tracking (SPATT) was performed in two bays of King George Island (KGI) in January 2013 and 2014. In addition, SPATT sampling was performed in Potter Cove during a one-year period from January 2014 until January 2015. Known toxigenic taxa were not firmly identified in plankton samples but there was microscopical evidence for background level presence of Dinophysis spp. in the area. This was consistent with environmental conditions during the sampling periods, especially strong mixing of the water column and low water temperatures that do not favor dinoflagellate proliferations. Due to the lack of significant abundance of thecate toxigenic dinoflagellate species in microplankton samples, no phycotoxins were found in net tow samples. In contrast, SPATT sampling revealed the presence of dissolved pectenotoxin-2 (PTX-2) and its hydrolyzed form PTX-2 seco acid in both bays and during the entire one-year sampling period. The presence of dissolved PTX in coastal waters of KGI is strong new evidence for the presence of PTX-producing species, i.e., dinoflagellates of the genus Dinophysis in the area. The presence of phycotoxins and their respective producers, even at the low background concentrations found in this study, may be the seed of possible proliferations of these species under changing environmental conditions. Furthermore, phycotoxins can be used as chemotaxonomic markers for a very specific group of plankton thus allowing to track the presence of this group over time.
Bird predation does not explain spatial variation in insect herbivory in a forest–tundra ecotone
Authors: Zverev Vitali , Zvereva Elena L. , Kozlov Mikhail V.
Published: February 2020

The contribution of bird predation to the spatial variations in insect herbivory remains imperfectly understood, especially in Arctic ecosystems. We experimentally tested the hypothesis that the differences in insect herbivory between tundra and forest biomes, and between plant life-forms in these biomes, are associated with differences in the intensity of bird predation on defoliating insects. We observed substantial variation in herbivory (0% to 20% of foliage lost) among nine forest, mountain tundra, and lowland tundra sites in the Kola Peninsula (northwestern Russia) and among five woody plant species, but we found no consistent differences in herbivory between biomes and between plant life-forms. Bird attacks on artificial caterpillars were tenfold more frequent in forest than in tundra, while bird exclusion effects on herbivory did not differ between biomes, and the intensities of bird predation measured by these two methods were not correlated. Bird exclusion led to increases in insect herbivory, and this effect was significant in trees and tall shrubs but was not significant in dwarf shrubs in either forest or tundra sites. Bird predation, as measured in bird exclusion experiments, increased with an increase in the level of foliar damage inflicted by insects in forests but not in tundra habitats. We conclude that bird predation generally decreases plant losses to insects in both forest and tundra habitats, but birds are unlikely to shape the spatial patterns of plant losses to insects in Arctic ecosystems.
Diets of European polecat Mustela putorius in Great Britain during fifty years of population recovery
Authors: Sainsbury Katherine A. , Shore Richard F. , Schofield Henry , Croose Elizabeth , Hantke Georg , Kitchener Andrew C. , McDonald Robbie A.
Published: February 2020

Following nineteenth-century declines, polecats Mustela putorius are recolonising Great Britain. Polecat diet relates to two potential risks to recovery. First, rabbits Oryctolagus cuniculus, which are important prey for polecats, have experienced extreme population fluctuations, with near extirpation due to myxomatosis in the 1950s, recovery in 1960s–1990s and declines in 1990s–2010s. Second, polecats are secondarily exposed to anticoagulant rodenticides by eating contaminated rodents, and the frequency of polecat exposure to rodenticides is increasing. We analysed stomach contents from 99 polecats collected in 2012–2016 and compared results with earlier studies. Lagomorphs were the most abundant prey (66% frequency of occurrence, 95% confidence interval 53–74%), followed by other mammals (12%, 4–18%), amphibians (10%, 3–16%) and birds (7%, 1–13%). Diet varied seasonally; lagomorph occurrence was highest in spring and summer and lowest in autumn. Dietary niche breadth was greater in the 1960s, when rabbits were scarce, than in other decades, but did not differ between the 1990s and 2010s, indicating that diets have not diversified with recent rabbit declines. This may be because rabbit abundance is not yet low enough to cause dietary diversification or because polecats were collected in areas where rabbits were still abundant. Rodents did not increase in diet between the 1990s and 2010s and still occur with < 10% frequency, indicating that rodents need not contribute much to diet to expose polecats to rodenticides. This potentially limits the effectiveness of management actions designed to minimise polecat exposure to contaminated rodent prey.
Reducing the Dependence of the Neural Network Function to Systematic Uncertainties in the Input Space
Authors: Wunsch Stefan , Jörger Simon , Wolf Roger , Quast Günter
Published: February 2020

Applications of neural networks to data analyses in natural sciences are complicated by the fact that many inputs are subject to systematic uncertainties. To control the dependence of the neural network function to variations of the input space within these systematic uncertainties, several methods have been proposed. In this work, we propose a new approach of training the neural network by introducing penalties on the variation of the neural network output directly in the loss function. This is achieved at the cost of only a small number of additional hyperparameters. It can also be pursued by treating all systematic variations in the form of statistical weights. The proposed method is demonstrated with a simple example, based on pseudo-experiments, and by a more complex example from high-energy particle physics.
Palladium-catalyzed diastereo- and enantioselective allylic alkylation of oxazolones with 1,3-dienes under base-free conditions
Authors: Yang Haijian , Xing Dong
Published: February 2020

Herein, we report a highly diastereo- and enantioselective allylic alkylation of oxazolones with 1,3-dienes by palladium-hydride catalyst under base-free conditions.
Force Plate Gait Analysis and Clinical Results after Tibial Plateau Levelling Osteotomy for Cranial Cruciate Ligament Rupture in Small Breed Dogs
Authors: Amimoto Hirokazu , Koreeda Tetsuaki , Ochi Yoshiyuki , Kimura Ryota , Akiyoshi Hideo , Nishida Hidetaka , Miyabayashi Takayoshi , Beale Brian S. , Hayashi Kei , Wada Naomi
Published: February 2020

Objective The aim of this study was to evaluate objective limb function using force plate gait analysis after tibial plateau levelling osteotomy (TPLO) in small breed dogs with cranial cruciate ligament rupture (CCLR).

Materials and Methods Small breed dogs (15 kg or less) with unilateral CCLR treated with TPLO were evaluated using symmetry index (SI) of peak vertical force (PVF), vertical impulse and vector magnitude at PVF performed preoperatively and at 1, 2, 4 and 6 months postoperatively after routine TPLO surgery.

Results Twelve dogs met the inclusion criteria. Hindlimb function was markedly improved after TPLO, with all three postoperative SI significantly higher after a month than preoperative values (p < 0.01). At 2 months after surgery, the SI was nearly normalized to 1.0 (preoperative SI: 0.50 ± 0.20, 0.44 ± 0.19 and 0.51 ± 0.19, and 2 months postoperative SI: 0.92 ± 0.16, 0.90 ± 0.18 and 0.92 ± 0.16 respectively). Complications were noted in two dogs (fibular fracture and a partial implant failure), neither of which required a revision surgery for acceptable functional recovery.

Conclusion The objective limb function of the affected hindlimb improved continuously after surgery and reached a near normal value at 6 months after surgery. It was suggested that TPLO for small breed dogs had good outcomes based on force plate gait analysis.
Smartphone Thermography for Lower Extremity Local Flap Perforator Mapping
Authors: Pereira Nicolás , Hallock Geoffrey G.
Published: February 2020

Background The versatile application of local perforator flaps for coverage throughout the lower extremity has already been well proven. Often a “free-style” approach has been used to design these flaps, as conventional imaging devices for perforator identification may be too expensive or unavailable. The recent adaptation of Smartphone thermal digital imaging may now prove to be a cheaper and more readily available means for identifying the requisite perforators that will sustain these local flaps.

Methods Over the past year, a prospective study was undertaken of all patients having a local perforator flap for coverage of a lower extremity defect. Twenty-eight local perforator flaps involving all subtypes were utilized in 25 patients. Smartphone thermography was used in all patients preoperatively to identify preferable perforator or vascular network “hot spots” that allowed appropriate flap design. Intraoperative and postoperative monitoring was similarly done for all flaps to determine outcomes.

Results All local perforator flaps were based on perforators identified using smartphone thermography. All flaps (23 or 82.1%) that the thermal digital image predicted 100% viability totally survived. Five flaps were predicted to have marginal viability, but two nevertheless survived completely while the others required only minor readjustments. Peninsular and keystone variety perforator flaps were those most commonly used.

Thermography always facilitated making the correct decision as to whether a proximal- or distal-based peninsular flap would be superior. Subfascial elevation of cool spots in keystone flaps were found to be least likely to interfere with flap perfusion.

Conclusion Smartphone thermography is an inexpensive and expeditious means for identification of “hot spots” that is always used by us to ensure perfusion to lower extremity perforator local flaps. This is a complementary technique for their safer design, harvest, and subsequent monitoring in conjunction with more complex screening tools as indicated.
Biomechanical and Histological Assessment of a Polyethylene Terephthalate Screw Retention Technology in an Ovine Metatarsal Fracture Model
Authors: Easley Jeremiah , Puttlitz Christian , Broomfield Cecily , Palmer Ross , Jones Alexander , McGilvray Kirk C.
Published: February 2020

Objective Screw loosening in fracture fixation poses a clinical risk which may lead to implant failure, particularly in poor bone quality. The objective of this study was to examine the effectiveness of a novel screw retention technology (SRT) for increased screw purchase in a large animal metatarsal fracture model.

Study Design This was a biomechanical, radiographic, and histological study utilizing an ovine metatarsal fracture model. Twenty-four sheep metatarsi underwent 3-mm ostectomies and were repaired with a nine-hole plate and 3.5-mm screws placed in oversized 3.5-mm holes to simulate worst case revision surgeries (i.e. no initial screw thread bone contact). Sheep were sacrificed at 3, 6 or 12 weeks (n = 6 each) post-operation. Post-sacrifice, each surgically implanted screw underwent either destructive mechanical testing or histomorphometric analyses.

Results Treated metatarsi showed improved screw retention and normal fracture healing. Significant improvement in breakout strength and pullout strength of screws treated with the SRT were found as a function of healing time. Histologically, bone ingrowth at the screw interface was also shown to significantly increase with healing time. Improvements in fracture healing, indicated by an increase in bone fraction and decrease in void space at the osteotomy, were also observed with healing time.

Conclusion The results demonstrate the effectiveness of the SRT as a method for improved screw retention in a rescue-screw type scenario.
C-Reactive Protein/Albumin Ratio as an Independent Predictor of Mortality in Critically Ill Pediatric Patients
Authors: Mohamed Shereen A. , ElHawary Rabab
Published: February 2020

It is necessary to stratify the risk of pediatric patients at the time of intensive care unit (ICU) admission and to predict their outcomes. This helps to allocate the scarce ICU resources to start the appropriate treatment. The objective of this study was to evaluate the prognostic value of C-reactive protein/albumin ratio on admission to pediatric intensive care unit (PICU) in predicting mortality, PICU length of stay, the need for mechanical ventilation, and the use of inotropic drugs. This cohort study was conducted at Pediatric Cairo University Hospital. The study included 178 critically ill children. Pediatric Risk of Mortality–III (PRISM-III) score was calculated; CRP and serum albumin levels were assessed within 24 hours from admission. The median CRP/albumin ratio was significantly higher in nonsurvivors than survivors (18.60 and 4.65, respectively). The CRP/albumin ratio at a cutoff of ≥25.83 had significant discriminatory power in predicting mortality (area under the curve [AUC] = 0.795 and p < 0.001) with 85.4% accuracy. Furthermore, CRP/albumin ratio alone showed a comparable discriminatory power to that of PRISM-III score (AUCs = 0.795 and 0.793, respectively). A multivariable logistic regression analysis revealed that each unit of increase in the CRP/albumin ratio increased the risk of mortality by 1.075 (odds ratio [OR] = 1.075). CRP/albumin ratio showed a significantly higher median in ventilated (6.86) compared with non-ventilated (5.22) patients. Patients supported with inotropes showed significantly higher median CRP/albumin ratio (11.70 and 3.68, respectively). CRP/albumin ratio at admission to PICU was a good independent predictor of mortality.
Transversus Abdominis Plane Blocks in Microsurgical Breast Reconstruction: A Systematic Review and Meta-analysis
Authors: Abdou Salma A. , Daar David A. , Wilson Stelios C. , Thanik Vishal
Published: February 2020

Background Transversus abdominis plane (TAP) blocks have been shown to significantly reduce pain and narcotic consumption following major abdominal surgeries. This study investigates the literature on their use in microsurgical breast reconstruction.

Patients and Methods A systematic review of TAP blocks in autologous breast reconstruction was performed.

Results Across 10 included studies, 174 patients (5 studies) received an intraoperative TAP block injection, 185 patients (4 studies) received a TAP catheter for intermittent postoperative analgesia, and 325 patients served as controls for a total of 684 included patients. The majority of TAP block delivery techniques were ultrasound guided (7/10 studies). Liposomal bupivacaine (LB) was the most commonly used analgesic (4 studies and139 patients) followed by conventional bupivacaine (3 studies and 105 patients). Eight studies found a significant reduction in oral, intravenous, and/or total morphine requirements in the TAP group when either the daily average and/or total inpatient consumption was compared with the control. Hospital length of stay was significantly shorter for patients undergoing single intraoperative TAP block injection with any analgesic as compared with standard narcotic-based protocols (mean difference= −0.95 days; 95% CI: −1.72 to −0.17 days; p = 0.02). Looking at TAP blocks specifically with LB, there was a mean decrease of 0.83 days as compared with the control, which was not statistically significant (95% CI: −1.90 to 0.25 days; p = 0.13).

Conclusion While the current data support the use of TAP blocks in autologous breast reconstruction, additional studies with more standardized protocols should be performed to determine the most optimal practice.
Impact of Sarcopenia on Outcomes of Autologous Head and Neck Free Tissue Reconstruction
Authors: Jones Alexander J. , Alwani Mohamedkazim M. , Novinger Leah J. , Pittelkow Eric , Bonetto Andrea , Sim Michael W. , Moore Michael G. , Mantravadi Avinash V.
Published: February 2020

Background Sarcopenia has been implicated as a positive predictor of postsurgical complications. Its role in head and neck (H&N) free flap reconstruction has yet to be examined. Our study aimed to determine the clinical impact of sarcopenia on postoperative outcomes in patients receiving autologous free tissue reconstruction for H&N cancer (HNC).

Methods A retrospective case–control study was conducted at our tertiary referral center. Patients with HNC who received oncologic resection followed by autologous free tissue reconstruction were included. Preoperative abdominal computed tomography (CT) imaging was analyzed at the third lumbar vertebra (L3) to calculate skeletal muscle cross-sectional area (CSA, cm2). Skeletal muscle index (SMI, cm2/m2) was calculated by normalizing CSA to patient height. Sarcopenia at L3 was defined as SMI ≤ 41.6 cm2/m2 for males and ≤ 32.0 cm2/m2 for females. Data analyses were performed to compare postoperative outcomes.

Results Of the 168 patients who met inclusion criteria, 47 patients (28.0%) were determined to have preoperative sarcopenia. The sarcopenic group was older (63 vs. 58 years, p = 0.017), had lower body mass index (BMI; 21.2 vs. 27.2, p < 0.001), had greater incidence of alcohol abuse (55.3 vs. 23.1%, OR = 4.11, p < 0.001). Intraoperatively, sarcopenic patients were found to have greater rates of blood transfusions (63.8 vs. 29.8%, p < 0.001). Postoperatively, sarcopenic patients had higher rates of pneumonia (p < 0.01), venous thromboembolism (p < 0.01), prolonged ventilation (p < 0.01), delirium (p < 0.01), fistula (p < 0.05), wound disruption (p < 0.05), and longer intensive care unit stays (p < 0.05). Sarcopenic patients were ultimately found to have higher overall rates of general postoperative complications (p < 0.001) and flap-specific complications (p < 0.01).

Conclusion Sarcopenia was found to be a predictor of postoperative complications in H&N free flap reconstruction, signifying its value as a negative prognostic factor in surgical outcomes. This study reflects level of evidence IV.
Postoperative Free Flap Breast Protocol Optimizing Resources and Patient Safety
Authors: Fadavi Darya , Haley Allison , Khavanin Nima , Kraenzlin Franca , Bos Tobias J. , Cho Brian H. , Carl Hannah M. , Bhat Deepa , Ostrander Benjamin T. , Manahan Michele A. , Rosson Gedge D. , Sacks Justin M.
Published: February 2020

Background As deep inferior epigastric artery perforator (DIEP) flaps have gained popularity in breast reconstruction, the postoperative care of these patients, including the appropriate hospital length-of-stay and the need for intensive care unit (ICU) admission, has become a topic of debate. At our institution, we have adopted a pathway that aims for discharge on postoperative day 3, utilizing continuous tissue oximetry without ICU admission. This study aims to evaluate outcomes with this pathway to assess its safety and feasibility in clinical practice.

Methods A retrospective review was performed of patients undergoing DIEP flap breast reconstruction between January 2013 and August 2014. Data of interest included patient demographics and medical history as well as complication rates and date of hospital discharge.

Results In total, 153 patients were identified undergoing 239 DIEP flaps. The mean age was 50 years (standard deviation [SD] = 10.2) and body mass index (BMI) 29.4 kg/m2 (SD = 5.2). Over the study period, the flap failure rate was 1.3% and reoperation rate 3.9%. Seventy-one percent of patients were discharged on postoperative day 3. Nine patients required hospitalization beyond 5 days. Theoretical cost savings from avoiding ICU admissions were $1,053 per patient.

Conclusion A pathway aiming for hospital discharge on postoperative day 3 without ICU admission following DIEP flap breast reconstruction can be feasibly implemented with an acceptable reoperation and flap failure rate.
Incidence, Predictors, and Adverse Outcomes of Extubation Failure in Young Children with Isolated Traumatic Brain Injury: A Prospective Observational Study
Authors: Hazarika Amarjyoti , Gupta Aakriti , Jain Kajal , Kajal Kamal
Published: February 2020

Background Mechanical ventilation is a life-saving mainstay of therapy in pediatric patients with isolated traumatic brain injury (iTBI). Because of the numerous complications and side effects associated with tracheal intubation, it is prudent to remove it as early as possible. Extubation failure and reintubation, however, are also associated with significant risks. Till date, there has been no comprehensive study on extubation failure in pediatric patients less than 5 years with iTBI.

Materials and Methods A prospective observational study was conducted in the trauma intensive care unit (TICU) of a tertiary care center. All the children with iTBI, aged 0 to 5 years, on mechanical ventilation for more than 24 hours, admitted to the TICU were included. Extubation failure was defined as the need for reintubation occurring within 24 hours of extubation. Only the first attempt at extubation was included in the analysis.

Results Pre-extubation paO2/FiO2 ratio < 310 mm Hg is a predictor for extubation failure. Mean base deficit postextubation were found to be 2 ± 0.9 and –0.2 ± 1 (p = 0.00) between success and failure groups, respectively. Similarly, postextubation systolic blood pressure was also high in the failure group than in the success group (113.8 ± 10.4 vs. 100.5 ± 7.4; p = 0.00).

Conclusions The incidence of first attempt extubation failure was 62.5%. Lower values of pre-extubation paO2/FiO2 ratio (ratio < 310 mm Hg) are a predictor for extubation failure. Developing predictive tools and optimizing extubation decisions lead to timely identification of patients at elevated risk of extubation failure.
Betaine-loaded CaCO3 microparticles improve survival of vitrified feline preantral follicles through higher mitochondrial activity and decreased reactive oxygen species
Authors: Brito D. C. C. , Domingues S. F. S. , Rodrigues A. P. R. , Silva L. M. , Alves K. A. , Wu X. , Francisco T. S. , Barroso Neto I. L. , Freire V. N. , Figueiredo J. R. , Pieczarka J. C. , Santos R. R.
Published: February 2020

Ovary fragments from six sexually mature cats were vitrified in the presence or absence of betaine or ascorbic acid, loaded (7.4 or 74µM betaine; 20 or 200µM ascorbic acid) or not (1mM betaine or 0.3mM ascorbic acid) into CaCO3 microparticles, and assessed for follicular morphology, oxidative stress and mitochondrial activity Feline ovarian tissue was successfully preserved after vitrification in the presence of 74µM betaine loaded in CaCO3 microparticles, as confirmed by morphological analysis and the density of preantral follicles and stromal cells, as well as by the increased mitochondrial activity and decreased production of reactive oxygen species.
Pre-expanded bipedicled visor flap: an ideal option for the reconstruction of upper and lower lip defects postburn in Asian males
Authors: Min Peiru , Li Jie , Brunetti Beniamino , Pu Zheming , Su Weijie , Xi Wenjing , Zhang Zheng , Salzillo Rosa , Feng Shaoqing , Zhang Yixin
Published: February 2020

Background

Reconstruction of upper and lower lip subunits is a complicated and elusive challenge. For patients affected by defects involving upper and lower lip subunits, a technique able to reconstruct both aesthetic units with matched colour, sufficient contours and similar texture would be ideal. In this study, we present our experience with upper and lower lip reconstruction using the pre-expanded bipedicled visor flap.

Methods

From January 2014 to January 2017, 12 male patients presenting with defects of the upper and lower lip subunits were treated using this surgical technique. After a period of expansion of the scalp flap of over 6 months, the bipedicled visor flap was raised from both the parietal regions and rotated to resurface the defect. Delay and section of the pedicle were then performed.

Results

Twelve male patients with postburn scars aged 22 to 48 years (mean: 34 years) were successfully treated with no major complications. The donor site was closed primarily in all cases. Subsequent flap debulking and minor revisions were performed under local anaesthesia between 6 and 12 months postoperatively.

Conclusions

The pre-expanded bipedicled visor flap provides an effective and reliable option for upper and lower lip reconstruction with excellent colour and texture. It is feasible to achieve these results simultaneously from a single donor site by using a pre-expanded bipedicled visor flap.
Moho depth of the British Isles: a probabilistic perspective
Authors: Licciardi A , England R W , Piana Agostinetti N , Gallagher K
Published: February 2020

We present a new Moho depth model of the British Isles and surrounding areas from the most up-to-date compilation of Moho depth estimates obtained from refraction, reflection and receiver function data. We use a probabilistic, trans-dimensional and hierarchical approach for the surface reconstruction of Moho topography. This fully data-driven approach allows for adaptive parametrization, assessment of relative importance between different data-types and uncertainties quantification on the reconstructed surface. Our results confirm the first order features of the Moho topography obtained in previous work such as deeper Moho (29–36 km) in continental areas (e.g. Ireland and Great Britain) and shallower Moho (12–22 km) offshore (e.g. in the Atlantic Ocean, west of Ireland). Resolution is improved by including recent available data, especially around the Porcupine Basin, onshore Ireland and Great Britain. NE trending features in Moho topography are highlighted above the Rockall High (about 28 km) and the Rockall Trough (with a NE directed deepening from 12 to about 20 km). A perpendicular SE oriented feature (Moho depth 26–28 km) is located between the Orkney and the Shetland, extending further SW in the North Sea. Onshore, our results highlight the crustal thinning towards the N in Ireland and an E–W oriented transition between deep (34 km) and shallow (about 28 km) Moho in Scotland. Our probabilistic results are compared with previous models showing overall differences around ±2 km, within the posterior uncertainties calculated with our approach. Bigger differences are located where different data are used between models or in less constrained areas where posterior uncertainties are high.
Silicon influences the localization and expression ofPhytophthora sojaeeffectors in interaction with soybean
Authors: Rasoolizadeh Aliyeh , Santhanam Parthasarathy , Labbé Caroline , Shivaraj Sheelavanta Matha , Germain Hugo , Bélanger Richard R
Published: February 2020

In plant–pathogen interactions, expression and localization of effectors in the aqueous apoplastic region play a crucial role in the establishment or suppression of pathogen development. Silicon (Si) has been shown to protect plants in several host–pathogen interactions, but its mode of action remains a source of debate. Its deposition in the apoplastic area of plant cells suggests that it might interfere with receptor–effector recognition. In this study, soybean plants treated or not with Si were inoculated with Phytophthora sojae and differences in the ensuing infection process were assessed through different microscopy techniques, transcript analysis of effector and defense genes, and effector (Avr6) localization through immunolocalization and fluorescence labeling. In plants grown without Si, the results showed the rapid (4 d post-inoculation) host recognition by P. sojae through the development of haustorium-like bodies, followed by expression and release of effectors into the apoplastic region. In contrast, Si treatment resulted in limited pathogen development, and significantly lower expression and presence of Avr6 in the apoplastic region. Based on immunolocalization and quantification of Avr6 through fluorescence labeling, our results suggest that the presence of Si in the apoplast interferes with host recognition and/or limits receptor–effector interactions, which leads to an incompatible interaction.
Segmenting the Universe into dynamically coherent basins
Authors: Dupuy Alexandra , Courtois Hélène M , Libeskind Noam I , Guinet Daniel
Published: February 2020

This paper explores in depth a watershed concept to partition the Universe, introduced in a previous Letter and applied to the Cosmicflows-3 observational data set. We present a series of tests conducted with cosmological dark matter simulations. In particular, we are interested in quantifying the evolution with redshift of large-scale structures when defined as segmented basins of attraction. This new dynamical definition in the field of measuring standard rulers demonstrates robustness since all basins show a density contrast δ above 1 (mean Universe density) independently of the simulation spatial resolution or the redshift. Another major finding is that density profiles of the basins show universality in slope. Consequently, there is a unique definition of what is a gravitational watershed at a large scale, which can be further used as a probe for cosmology studies.
Conceptual Aspects of Global Value Chains
Authors: Antràs Pol
Published: February 2020

This article offers an overview of some key conceptual aspects associated with the rise of global value chains (GVCs). It outlines a series of alternative interpretations and definitions of what the rise of GVCs entails, and it traces the implications of these alternative conceptualizations for the measurement of the phenomenon, as well as for elucidating the key determinants and implications of GVC participation, both at the country level and at the firm level. In the process, it offers some speculative thoughts about the future of GVCs in light of the advent of an array of new technologies.
Directed evolution ofAnabaena variabilisphenylalanine ammonia-lyase (PAL) identifies mutants with enhanced activities
Authors: Mays Zachary JS , Mohan Karishma , Trivedi Vikas D , Chappell Todd C , Nair Nikhil U
Published: February 2020

There is broad interest in engineering phenylalanine ammonia-lyase (PAL) for its biocatalytic applications in industry (fine-chemicals and natural product synthesis) and medicine (phenylketoruria/PKU and cancer treatment). While site-specific mutagenesis has been employed to improve PAL stability or substrate specificity, a more comprehensive mutational landscape has yet to be explored for this class of enzymes. Here, we report development of a directed evolution technique to engineer PAL enzymes. Central to this approach is a high-throughput enrichment that couplesE. coligrowth to PAL activity. Using the clinically-relevant PAL fromAnabaena variabilis, which is used on the formulation of pegvaliase for PKU therapy, we identified mutations at residues previously unknown as relevant for function that increase turnover frequency almost twofold after only a single round of engineering. This work demonstrates the power our technique for ammonia-lyase enzyme engineering.
Predicting and Visualizing STK11 Mutation in Lung Adenocarcinoma Histopathology Slides Using Deep Learning
Authors: Hong Runyu , Liu Wenke , Fenyö David
Published: February 2020

Studies have shown that STK11 mutation plays a critical role in affecting the lung adenocarcinoma (LUAD) tumor immune environment. By training an Inception-Resnet-v2 deep convolutional neural network model, we were able to classify STK11-mutated and wild type LUAD tumor histopathology images with a promising accuracy (per slide AUROC=0.795). Dimensional reduction of the activation maps before the output layer of the test set images revealed that fewer immune cells were accumulated around cancer cells in STK11-mutation cases. Our study demonstrated that deep convolutional network model can automatically identify STK11 mutations based on histopathology slides and confirmed that the immune cell density was the main feature used by the model to distinguish STK11-mutated cases.
Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation
Authors: Choudry Fizzah A , Bagger Frederik Otzen , Macaulay Iain C , Farrow Samantha , Burden Frances , Kempster Carly , McKinney Harriet , Olsen Lars R , Huang Ni , Downes Kate , Voet Thierry , Uppal Rakesh , Martin John F , Mathur Anthony , Ouwehand Willem H , Laurenti Elisa , Teichmann Sarah A , Frontini Mattia
Published: February 2020

In the current understanding of adult bone marrow hematopoiesis, megakaryocytes (MKs) originate from cells immuno-phenotypically indistinguishable from hematopoietic stem cells (HSCs), bypassing intermediate progenitors. Here, we use single cell RNA sequencing to characterize HSCs and MKs from human bone marrow, to investigate MK lineage commitment and maturation. We identify two MK primed HSC clusters exhibiting unique differentiation kinetics, at least one of which is used in steady state and stress thrombopoiesis. By analyzing transcriptional signatures we show that human bone marrow MKs originate from MK primed HSC subpopulations, supporting the notion that these display exclusive priming for MK differentiation. We show that transcriptional programs change with increasing MK ploidy, where genes upregulated in high ploidy states may have functional relevance in platelet production. Finally, we highlight the presence of a specific transcriptional signature in MKs from individuals with myocardial infarction, supporting the aberration of MK differentiation in this thrombotic state.
Stomatal density affects gas diffusion and CO2assimilation dynamics in Arabidopsis under fluctuating light
Authors: Sakoda Kazuma , Yamori Wataru , Shimada Tomoo , Sugano Shigeo S. , Hara-Nishimura Ikuko , Tanaka Yu
Published: February 2020

Stomatal density (SD) is closely associated with photosynthetic and growth characteristics in plants. In the field, light intensity can fluctuate drastically throughout a day. The objective of the present study is to examine how the change inSDaffects stomatal conductance (gs) and CO2assimilation rate (A) dynamics, biomass production, and water use under fluctuating light. Here, we compared the photosynthetic and growth characteristics under constant and fluctuating light among four lines ofArabidopsis thaliana(L.): a wild-type (WT), aSTOMAGEN/EPFL9-overexpressing line,STOMAGEN/EPFL9-silencing line, and anEPIDERMAL PATTERNING FACTOR 1knockout line (epf1). LowerSDresulted in faster response ofAowing to the faster response ofgsto fluctuating light and higher water use efficiency without decreasingA. HigherSDresulted in a faster response ofAbecause of the higher initialgs.epf1, with a moderate increase inSD, showed the larger carbon gain, attributable to the high capacity and fast response ofA, yielding higher biomass production than WT under fluctuating light. The present study suggests that higherSDcan be beneficial to improve biomass production in the plant under field conditions.
HOW TO MEASURE THE INFLUENCE OF LANDSCAPE ON POPULATION GENETIC STRUCTURE: DEVELOPING RESISTANCE SURFACES USING A PATTERN-ORIENTED MODELING APPROACH
Authors: Souza Kelly , Pinto-Ledezma Jesús N. , de Campos Telles Mariana Pires , Soares Thannya Nascimento , Chaves Lazaro José , Ruas Clarissa Bonafé Gaspar , Dobrovolski Ricardo , Diniz-Filho José Alexandre Felizola
Published: February 2020

There are several approaches to understand how a landscape, with its several components, affects the genetic population structure by imposing resistance to gene flow. Here we propose the creation of resistance surfaces using a Pattern-Oriented Modeling approach to explain genetic differentiation, estimated by pairwise FST, among “Baruzeiro” populations (Dipteryx alata), a tree species widely distributed in Brazilian Cerrado. To establish the resistance surface, we used land use layers from the area in which the 25 “Baruzeiro” populations were sampled, generating 10000 resistance surfaces. To establish the resistance surface, we used land use layers from the area in which the 25 “Baru” populations were sampled, generating 10000 resistance surfaces. We randomized the cost values for each landscape component between 0 and 100. We use these surfaces to calculate pairwise matrices of the effective resistance among populations. Mantel test revealed a correlation of pairwise FST with a geographical distance equal to r = 0.48 (P < 0.001), whereas the Mantel correlations between pairwise FST and the generated resistance matrices ranged between r = −0.2019 and r= 0.6736. Partial regression on distance matrices was used to select the resistance matrix that provided the highest correlation with pairwise FST, based on the AIC criterion. The selected models suggest that the areas with lower resistance are characterized as natural savanna habitats of different forms, mainly arboreal dense savannas. In contrast, roads, big rivers, and agricultural lands cause higher resistance to gene flow.
Genome-wide analysis ofEscherichia colifitness determinants in a cross-feeding mutualism withRhodopseudomonas palustris
Authors: LaSarre Breah , Deutschbauer Adam M. , Love Crystal E. , McKinlay James B.
Published: February 2020

Microbial interactions abound in natural ecosystems and shape community structure and function. Substantial attention has been given to cataloging mechanisms by which microbes interact, but there is a limited understanding of the genetic landscapes that promote or hinder microbial interactions. We previously developed a mutualistic coculture pairingEscherichia coliandRhodopseudomonas palustris, whereinE. coliprovides carbon toR. palustrisin the form of glucose fermentation products andR. palustrisfixes N2gas and provides nitrogen toE. coliin the form of NH4+. The stable coexistence and reproducible trends exhibited by this coculture make it ideal for interrogating the genetic underpinnings of a cross-feeding mutualism. Here, we used random barcode transposon sequencing (RB-TnSeq) to conduct a genome-wide search forE. coligenes that influence fitness during cooperative growth withR. palustris. RB-TnSeq revealed hundreds of genes that increased or decreasedE. colifitness in a mutualism-dependent manner. Some identified genes were involved in nitrogen sensing and assimilation, as expected given the coculture design. The other identified genes were involved in diverse cellular processes, including energy production and cell wall and membrane biogenesis. Additionally, we discovered unexpected purine cross-feeding fromR. palustristoE. coli, with coculture rescuing growth of anE. colipurine auxotroph. Our data provide insight into the genes and gene networks that can influence a cross-feeding mutualism and underscore that microbial interactions are not necessarily predictablea priori.

IMPORTANCE

Microbial communities impact life on earth in profound ways, including driving global nutrient cycles and influencing human health and disease. These community functions depend on the interactions that resident microbes have with the environment and each other. Thus, identifying genes that influence these interactions will aid the management of natural communities and the use of microbial consortia as biotechnology. Here, we identified genes that influencedEscherichia colifitness during cooperative growth with a mutualistic partner,Rhodospeudomonas palustris. Although this mutualism centers on the bidirectional exchange of essential carbon and nitrogen,E. colifitness was positively and negatively affected by genes involved in diverse cellular processes. Furthermore, we discovered an unexpected purine cross-feeding interaction. These results contribute knowledge on the genetic foundation of a microbial cross-feeding interaction and highlight that unanticipated interactions can occur even within engineered microbial communities.
Inactivating porcine coronavirus before nuclei acid isolation with the temperature higher than 56 °C damages its genome integrity seriously
Authors: Zhang Qingxin , Zhao Qingshun
Published: February 2020

2019-Novel Coronavirus (2019-nCoV) is the pathogen of Corona Virus Disease 2019. Nucleic acid detection of 2019-nCoV is one of the key indicators for clinical diagnosis. However, the positive rate is only 30-50%. Currently, fluorescent quantitative RT-PCR technology is mainly used to detect 2019-nCoV. According to “The Laboratory Technical Guidelines for Detection 2019-nCoV (Fourth Edition)” issued by National Health and Commission of China and “The Experts’ Consensus on Nucleic Acid Detection of 2019-nCoV” released by Chinese Society of Laboratory Medicine, the human samples must be placed under 56°C or higher to inactivate the viruses in order to keep the inspectors from virus infection before the nucleic acids were isolated as the template of qRT-PCR. In this study, we demonstrated that the virus inactivation treatment disrupts its genome integrity seriously when using porcine epidemic diarrhea virus (vaccine), a kind of coronavirus, as a model. Our results showed that only 50.11% of the detectable viral templates left after the inactivation of 56 °C for 30 minutes and only 3.36% left after the inactivation of 92 °C for 5 minutes when the samples were preserved by Hank’s solution, one of an isotonic salt solutions currently suggested. However, the detectable templates of viral nucleic acids can be unchanged after the samples were incubated at 56 °C or higher if the samples were preserved with an optimized solution to protect the RNA from being disrupted. We therefore highly recommend to carry out systematic investigation on the impact of high temperature inactivation on the integrity of 2019-nCoV genome and develop a sample preservation solution to protect the detectable templates of 2019-nCoV nucleic acids from high temperature inactivation damage.
A stronger transcription regulatory circuit of HIV-1C drives the rapid establishment of latency with implications for the direct involvement of Tat
Authors: Chakraborty Sutanuka , Kabi Manisha , Ranga Udaykumar
Published: February 2020

The magnitude of transcription factor binding site variation emerging in HIV-1C, especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong LTR? We constructed panels of sub-genomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. We found surprisingly that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.

Importance

Over the past 10-15 years, HIV-1C has been evolving rapidly towards gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive for HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and a concomitant strong, positive transcriptional feedback is the primary question we attempted to address in the present manuscript. The role Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype C (HIV-1C) offers crucial leads towards Tat possessing a dual-role in serving both as transcriptional activator and repressor at different phases of the viral infection of the cell. The leads we offer through the present work have significant implications for HIV-1 cure research.