bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fungal evolution: cellular, genomic and metabolic complexity
Authors: Naranjo‐Ortiz Miguel A. , Gabaldón Toni 
Published: April 2020

ABSTRACTThe question of how phenotypic and genomic complexity are inter‐related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
Uptake of positron emission tomography tracers reflects the tumor immune status in esophageal squamous cell carcinoma
Authors: Kuriyama Kengo , Higuchi Tamami , Yokobori Takehiko , Saito Hideyuki , Yoshida Tomonori , Hara Keigo , Suzuki Shigemasa , Sakai Makoto , Sohda Makoto , Higuchi Tetsuya , Tsushima Yoshito , Asao Takayuki , Kaira Kyoichi , Kuwano Hiroyuki , Shirabe Ken , Saeki Hiroshi 
Published: April 2020

AbstractThe relationship between the local immune status and cancer metabolism regarding 18F‐FDG and 18F‐FAMT uptake in esophageal squamous cell carcinoma (ESCC) remains unknown. The present study examined the correlations between tumor immune status, clinicopathological factors, and positron emission tomography (PET) tracer uptake in ESCC. Forty‐one ESCC patients who underwent 18F‐FDG PET and 18F‐FAMT PET before surgery were enrolled in the study. Immunohistochemistry was conducted for programmed death 1 (PD‐1), CD8, Ki‐67, CD34, GLUT1 (18F‐FDG transporter) and LAT1 (18F‐FAMT transporter). ESCC specimens with high tumoral PD‐L1 and high CD8‐positive lymphocytes were considered to have “hot tumor immune status.” High PD‐L1 expression (53.7%) was significantly associated with tumor/lymphatic/venous invasion (P = 0.028, 0.032 and 0.018), stage (P = 0.041), CD8‐positive lymphocytes (P < 0.001), GLUT1 (P < 0.001), LAT1 expression (P = 0.006), Ki‐67 labelling index (P = 0.009) and CD34‐positive vessel counts (P < 0.001). SUVmax of 18F‐FDG was significantly higher in high PD‐L1 cases than in low PD‐L1 cases (P = 0.009). SUVmax of 18F‐FAMT was significantly higher in high PD‐L1 (P < 0.001), high CD8 (P = 0.012) and hot tumor groups (P = 0.028) than in other groups. High SUVmax of 18F‐FAMT (≥4.15) was identified as the only predictor of hot tumor immune status. High PET tracer uptake was significantly associated with cancer aggressiveness and hot tumor immune status in ESCC. PET imaging may be an effective tool to predict tumor immune status in ESCC with respect to immune checkpoint inhibitor sensitivity.
Treatment of chronic inflammatory demyelinating polyradiculoneuropathy patients with antibodies against paranodal proteins
Authors: Iijima Masahiro 
Published: April 2020

AbstractChronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is an acquired immune‐mediated polyneuropathy characterized by relapsing or steadily progressive clinical course. A major feature of the syndrome is that it encompasses several pathogeneses, and it is actually assumed that both cellular and humoral immunity can be involved with superiority depending on the particular subtype. Although cellular immunity typified by macrophage‐derived demyelination can play an essential role in classical CIDP, other pathogeneses that involve humoral immunity, such as autoantibodies targeting node of Ranvier proteins (neurofascin155: NF155; contactin1: CNTN1; contactin‐associated protein1: Caspr1; and neurofascin186/140: NF186/140), can bring about functional demyelination and have been discovered in approximately 5–15% of CIDP patients. Interestingly, such antibodies commonly belong to the immunoglobulin G4 (IgG4) subclass, and thus lack complement‐binding sites and compete with other IgG subclasses for the antigens. Patients with these IgG4 autoantibodies share clinical presentations to a certain extent, and anti‐NF155 and anti‐CNTN1 antibodies are representative examples. Patients with these IgG4 subclass antibodies fulfill the conservative diagnostic criteria for CIDP: distal‐dominant weakness, tremor and sensory ataxia. These patients also show poor responses to conventional first‐line therapeutics, and are non‐responders to intravenous immunoglobulins in particular. Therefore, novel treatment strategies other than first‐line therapies are awaited, and to date, small retrospective studies and several case reports have suggested the efficacy of rituximab. Accordingly, the Efficacy and Safety of Rituximab in Refractory CIDP Patients with IgG4 Autoantibodies trial, a prospective trial investigating the efficacy and safety of rituximab, is currently in progress.
In the interest of saving: Refugee‐led microfinance in Kampala, Uganda
Authors: Easton‐Calabria Evan , Hakiza Robert 
Published: April 2020

ABSTRACTMotivationWhile livelihoods are increasingly promoted for refugees in long‐term situations of displacement, refugees can rarely access microfinance loans—the very start‐up capital generally considered necessary for creating businesses. Yet across Kampala, Uganda, refugees meet to place small amounts of money into group savings and take out and repay microloans.PurposeThis article sheds light on this underexplored phenomenon through an empirical study of refugee‐led microfinance groups in Kampala and an overview of the existing local landscape of refugee‐serving organizations and microfinance institutions providing loans. We analytically reflect on the role of trust in executing microfinance programmes both for and by refugees.Approach and MethodsWe conducted snowball and purposive sampling, semi‐structured qualitative interviews, focus group discussions, and non‐participant observation.FindingsOur study found that refugee‐led microfinance groups have created a loan structure that is successful for refugees—because it was developed by refugees—with low default rates. This success is underpinned by strong community trust between members. These groups access vulnerable populations important to humanitarian organizations, including women, single mothers, unregistered refugees and the very poor. However, despite filling an important gap in livelihoods assistance—the provision of business capital—refugee‐led microfinance groups lack large amounts of capital to loan members, and do not feel they provide adequate business, livelihoods and financial literacy trainings.Policy ImplicationsOur findings suggest that non‐governmental organizations (NGOs) should support existing groups through offering safe spaces to hold meetings, and with financial and business trainings. Debunking stereotypes of refugees held by financial providers, and advocating for refugees’ financial rights remains crucial. Providing loan capital to groups to enable members to take out larger loans may offer another means of support, but collaboration between formal microfinance institutions or NGOs and refugee‐led groups must reinforce rather than devalue the networks of trust that contribute to grassroots savings and loan groups’ success.
R‐DHA‐oxaliplatin (R‐DHAOx) versus R‐DHA‐cisplatin (R‐DHAP) regimen in B‐cell lymphoma treatment: A eight‐year trajectory study
Authors: Lacout Carole , Orvain Corentin , Seegers Valérie , De Vries Manon , Mercier Mélanie , Farhi Jonathan , Clavert Aline , Thepot Sylvain , Moles Marie‐Pierre , Ifrah Norbert , Hunault‐Berger Mathilde , Tanguy‐Schmidt Aline 
Published: April 2020

AbstractBackgroundThe R‐DHAP regimen (rituximab, cisplatin, dexamethasone, and high‐dose cytarabine) is standardly used to treat relapsed Non‐Hodgkin lymphoma (NHL). Despite scarce data, cisplatin is frequently substituted with oxaliplatin (R‐DHAOx) to avoid nephrotoxicity. We compared nephrotoxicity of cisplatin and oxaliplatin based on creatinine‐based trajectory modeling.MethodsAll patients with NHL treated by R‐DHAP or R‐DHAOx in Angers hospital between January 01, 2007, and December 31, 2014, were included. Patients received cisplatin 100 mg/m2 or oxaliplatin 130 mg/m2 (d1) with cytarabine (2000 mg/m2, two doses, d2), dexamethasone (40 mg, d1‐4), and rituximab (375 mg/m2, d1). Creatinine levels were recorded before each cycle. Individual profiles of trajectories were clustered to detect homogeneous patterns of evolution.ResultsTwenty‐two patients received R‐DHAP, 35 R‐DHAOx, 6 switched from R‐DHAP to R‐DHAOx due to nephrotoxicity. Characteristics of patients were similar between two groups. Patients receiving R‐DHAP experienced more severe renal injury than patients receiving R‐DHAOx (68% vs. 7.7%, P < .001). Two homogeneous clusters appeared: cluster A, with a majority of R‐DHAOx (32, 91.4%), was less nephrotoxic than B, with a majority of R‐DHAP (19, 86.4%), with a decreased average serum creatinine level (P < .0001). There were no other differences between clusters.ConclusionsOur study confirms that R‐DHAOx regimen causes less nephrotoxicity than R‐DHAP regimen.
Modified Delphi study of decision‐making around treatment sequencing in relapsing–remitting multiple sclerosis
Authors: Piena M. A. , Schoeman O. , Palace J. , Duddy M. , Harty G. T. , Wong S. L. 
Published: April 2020

Background and purposeExisting effectiveness models of disease‐modifying drugs (DMDs) for relapsing–remitting multiple sclerosis (RRMS) evaluate a single line of treatment; however, RRMS patients often receive more than one lifetime DMD. To develop treatment sequencing models grounded in clinical reality, a detailed understanding of the decision‐making process regarding DMD switching is required. Using a modified Delphi approach, this study attempted to reach consensus on modelling assumptions.MethodsA modified Delphi technique was conducted based on three rounds of discussion amongst an international group of 10 physicians with expertise in RRMS.ResultsThe panel agreed that the expected time from disease onset to Expanded Disability Status Scale 6.0 is a proxy for disease severity as well as suitable for classifying severity into three groups. A modelled clinical decision rule regarding the timing of switching should contain at least the time between relapses, magnetic resonance imaging outcomes and the occurrence/risk of adverse events. The experts agreed that the assessment of adverse event risk for a DMD is dependent on disease severity, with more risks accepted when the patient’s disease is more severe. The effectiveness of DMDs conditional on their position in a sequence and/or disease duration was discussed: there was consensus on some statements regarding this topic but these were accompanied by a high degree of uncertainty due to considerable knowledge gaps.ConclusionUseful insights into the medical decision‐making process regarding treatment sequencing in RRMS were obtained. The knowledge gained has been used to validate the main modelling concepts and to further generate clinically meaningful results.
Estimating the contribution of Greenland Halibut (Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping‐by‐sequencing: Sex and time matter
Authors: Carrier Emilie , Ferchaud Anne‐Laure , Normandeau Eric , Sirois Pascal , Bernatchez Louis 
Published: April 2020

AbstractIdentification of stocks and quantification of their relative contribution to recruitment are major objectives toward improving the management and conservation of marine exploited species. Next‐generation sequencing allows for thousands of genomic markers to be analyzed, which provides the resolution needed to address these questions in marine species with weakly differentiated populations. Greenland Halibut (Reinhardtius hippoglossoides) is one of the most important exploited demersal species throughout the North Atlantic, in particular in the Gulf of St. Lawrence, Canada. There, two nurseries are known, the St. Lawrence Estuary and the northern Anticosti Island, but their contribution to the renewal of stocks remains unknown. The goals of this study were (a) to document the genetic structure and (b) to estimate the contribution of the different identified breeding stocks to nurseries. We sampled 100 juveniles per nursery and 50 adults from seven sites ranging from Saguenay Fjord to offshore Newfoundland, with some sites sampled over two consecutive years in order to evaluate the temporal stability of the contribution. Our results show that after removing sex‐linked markers, the Estuary/Gulf of St. Lawrence represents a single stock which is genetically distinct from the Atlantic around Newfoundland (FST = 0.00146, p‐value = .001). Population assignment showed that recruitment in both nurseries is predominantly associated with the St. Lawrence stock. However, we found that the relative contribution of both stocks to the nurseries is temporally variable with 1% contribution of the Newfoundland stock one year but up to 33% for the second year, which may be caused by year‐to‐year variation in larval transport into the Gulf of St. Lawrence. This study serves as a model for the identification of stocks for fisheries resources in a context where few barriers to dispersal occur, in addition to demonstrating the importance of considering sex‐linked markers and temporal replicates in studies of population genomics.
Assessing the importance of autistic attributes for autism screening
Authors: Akyol Kemal 
Published: April 2020

AbstractAutistic Spectrum Disorder (ASD) is a cognitive disease which leads to the loss of linguistic, communicative, cognitive, and social skills and abilities. Patients with ASD have diverse troubles such as sleeping problems. The role of genetic and environmental factors is of great importance in its pathophysiology. Early diagnosis provides an improved overall mental health of the patients. This study aimed to identify the important attributes for the best detection of this disorder in children, adolescents and adults. To achieve this aim, Recursive Feature Elimination and Stability Selection methods that consider important attributes for target class were proposed. The attributes collected from autism screening methods and other attributes such as age and gender were examined for the disease. The results verified the combining of feature selection method and machine learning algorithm within the frame of accuracy, sensitivity and specificity evaluation metrics.
Genome‐wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin–antitoxin systems as a major substrate class
Authors: Ziemski Michal , Leodolter Julia , Taylor Gabrielle , Kerschenmeyer Anne , Weber‐Ban Eilika 
Published: April 2020

In Mycobacterium tuberculosis (Mtb), the Clp protease degradation pathway, mediated by the modular ClpCP and ClpXP protease complexes, is essential for growth and presents an attractive drug target. Employing a bacterial adenylate cyclase two‐hybrid (BACTH) screening approach that we adapted to screen the proteome of an Mtb ORF library, we identify protein interaction partners of the ClpC1 chaperone on a genome‐wide level. Our results demonstrate that bipartite type II toxin–antitoxin (TA) systems represent a major substrate class. Out of the 67 type II TA systems known in Mtb, 25 appear as ClpC1 interaction partners in the BACTH screen, including members of the VapBC, MazEF, and ParDE families, as well as a RelBE member that was identified biochemically. We show that antitoxins of the Vap and Rel families are degraded by ClpCP in vitro. We also demonstrate that ClpCP is responsible for mediating the N‐end rule pathway, since the adaptor protein ClpS supports ClpC‐dependent degradation of an N‐end rule model substrate in vitro.
Global patterns and controlling factors of soil nitrification rate
Authors: Li Zhaolei , Zeng Zhaoqi , Tian Dashuan , Wang Jinsong , Fu Zheng , Zhang Fangyue , Zhang Ruiyang , Chen Weinan , Luo Yiqi , Niu Shuli 
Published: April 2020

AbstractSoil nitrification, an important pathway of nitrogen transformation in ecosystems, produces soil nitrate that influences net primary productivity, while the by‐product of nitrification, nitrous oxide, is a significant greenhouse gas. Although there have been many studies addressing the microbiology, physiology, and impacting environment factors of soil nitrification at local scales, there are very few studies on soil nitrification rate over large scales. We conducted a global synthesis on the patterns and controlling factors of soil nitrification rate normalized at 25°C by compiling 3,140 observations from 186 published articles across terrestrial ecosystems. Soil nitrification rate tended to decrease with increasing latitude, especially in the Northern Hemisphere, and varied largely with ecosystem types. The soil nitrification rate significantly increased with mean annual temperature (MAT), soil nitrogen content, microbial biomass carbon and nitrogen, soil ammonium, and soil pH, but decreased with soil carbon:nitrogen and carbon:nitrogen of microbial biomass. The total soil nitrogen content contributed the most to the variations of global soil nitrification rate (total coefficient = 0.29) in structural equation models. The microbial biomass nitrogen (MBN; total coefficient = 0.19) was nearly of equivalent importance relative to MAT (total coefficient = 0.25) and soil pH (total coefficient = 0.24) in determining soil nitrification rate, while soil nitrogen and pH influenced soil nitrification via changing soil MBN. Moreover, the emission of soil nitrous oxide was positively related to soil nitrification rate at a global scale. This synthesis will advance our current understanding on the mechanisms underlying large‐scale variations of soil nitrification and benefit the biogeochemical models in simulating global nitrogen cycling.
Wideband frequency tunability of CaCu3Ti4O12‐based dielectric resonator antennas via the addition of glass
Authors: Ab Rahman Mohd Fariz , Ain Mohd Fadzil , Mohamad Hasmaliza , Mohamed Julie Juliewatty , Hassan Siti Roshayu , Ahmad Zainal Arifin 
Published: April 2020

AbstractIn this study, DRAs produced using CaCu3Ti4O12 (CCTO) as a high dielectric material (εr) was added with BaO–SrO–Nb2O5–B2O3–SiO2 (BSNBS) glass for possible tunability in a wideband frequency range. BSNBS glass (0.01‐1 wt%) was mixed with CCTO powders (calcined) and compacted at 250 MPa into mixed‐powder pellets. All the green body samples were then sintered at 1040°C for 10 hours. The wideband frequency tunability, measured using a network analyzer, showed that the addition of ≤0.05 wt% BSNBS glass decreased the resonance frequency from 9.51 to 9.33 GHz; later, the values increased to 9.89 GHz when BSNBS content was > 0.05 wt%. The εr of each sample was around 11‐36 when measured at 9.5‐11.8 GHz. The radiation pattern of CCTO for each sample that had been set up as a DRA radiated the signal equally or nearly identical to each other. Furthermore, the addition of BSNBS glass produced micrographs with finer grains, improved the density and reduced the porosity of the composite. Therefore, the addition of the BSNBS glass is a successful aid in the wideband frequency tunability of pure CCTO‐based ceramics when used as DRAs.
A home made of wood: Consumer experiences of wooden building materials
Authors: Viholainen Noora , Kylkilahti Eliisa , Autio Minna , Toppinen Anne 
Published: April 2020

AbstractHaving a home is a central part of the everyday consumer experience. In our study, we focus on Finnish homeowners who have recently bought an apartment in a multi‐family timber‐framed building. With its merits in sustainability, the number of timber buildings in less‐traditional urban applications is increasing, yet, research on living in a wooden home is scarce. To fill this gap, the study analyses how homeowners perceive the wooden material before and after living in a wooden home for one year. Thus, besides the acquisition of a home, the study examines the consumers' appropriation processes and aims to gain insight into the cultural sense‐making behind the appreciation of wooden homes. The results of this qualitative study indicate that traditions and memories related to wood affect consumers' appreciations, for example, regarding the cosiness of a wooden home. The consumers discussed the weaknesses assigned to wood, such as fire and moisture susceptibility, yet, they considered them to concern all construction materials, not only wood. After habitation for one year, the usability of the home becomes particularly relevant, including the ease with which shelves can be mounted onto the walls, enjoying the echoless soundscape, and living with clicking sounds and vibrating floors. The study suggests that the meanings of consumers' daily experiences concerning the usability of wooden buildings are under negotiation and cannot be reduced simply into positive or negative but carry elements of both.
Surgical details and renal function change after robot‐assisted partial nephrectomy
Authors: Shin Teak Jun , Song Cheryn , Kim Choung‐Soo , Ahn Hanjong 
Published: April 2020

ObjectivesTo investigate whether differences in surgical details during robot‐assisted partial nephrectomy impact postoperative renal function.MethodsPatient, tumor and perioperative characteristics of 751 patients who underwent robot‐assisted partial nephrectomy were analyzed with respect to the difference in ipsilateral glomerular filtration rate measured by diethylenetetramine pentaacetic acid renal scan. Detailed surgical methods defined for tumor excision (cutting vs splitting), hemostasis (suturing vs clipping) and renorrhaphy (continuous vs interrupted) were analyzed for early glomerular filtration rate decline and long‐term recovery.ResultsThe glomerular filtration rate of the entire cohort decreased by 9.8 mL/min/1.73 m2 (22%) at 3 months postoperatively, gradually increasing thereafter. The recovery slope was 1.7 mL/min/1.73 m2/year during a median follow‐up period of 23.0 months. Early glomerular filtration rate decline was more pronounced in the cutting group (23.5 vs 20.1%, P = 0.009). Clipping was associated with less glomerular filtration rate decline throughout the observation period, and the recovery slope was also significantly higher (2.7 vs 1.1 mL/min/1.73 m2/year). In multivariate analysis, early decline was associated with age, preoperative glomerular filtration rate, parenchymal volume loss and ischemia >25 min. With respect to long‐term recovery, suturing had the greatest adverse impact (β = −5.060, P < 0.0001, 95% confidence interval −7.709, −2.411) in addition to parenchymal volume reduction and early decline. In the propensity‐matched cohort accounting for differences in tumor size and complexity, suturing was persistently associated with a significant glomerular filtration rate decline until >2 years after surgery.ConclusionsHemostatic sutures during robot‐assisted partial nephrectomy might interfere with long‐term renal function recovery irrespective of parameters that determine the initial function change. As the splitting method reduces the use of sutures, modifying these details might help preserve renal function.