bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source
Authors: Sierra Raymond G. , Batyuk Alexander , Sun Zhibin , Aquila Andrew , Hunter Mark S. , Lane Thomas J. , Liang Mengning , Yoon Chun Hong , Alonso-Mori Roberto , Armenta Rebecca , Castagna Jean-Charles , Hollenbeck Michael , Osier Ted O. , Hayes Matt , Aldrich Jeff , Curtis Robin , Koglin Jason E. , Rendahl Theodore , Rodriguez Evan , Carbajo Sergio , Guillet Serge , Paul Rob , Hart Philip , Nakahara Kazutaka , Carini Gabriella , DeMirci Hasan , Dao E. Han , Hayes Brandon M. , Rao Yashas P. , Chollet Matthieu , Feng Yiping , Fuller Franklin D. , Kupitz Christopher , Sato Takahiro , Seaberg Matthew H. , Song Sanghoon , van Driel Tim B. , Yavas Hasan , Zhu Diling , Cohen Aina E. , Wakatsuki Soichi , Boutet Sébastien 
Published: February 2019

The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from LCLS at atmospheric conditions to overcome radiation damage limitations in biological measurements. It is also capable of performing various time-resolved measurements. The MFX design consists of a versatile base system capable of supporting multiple methods, techniques and experimental endstations. The primary techniques supported are forward scattering and crystallography, with capabilities for various spectroscopic methods and time-resolved measurements. The location of the MFX instrument allows for utilization of multiplexing methods, increasing user access to LCLS by running multiple experiments simultaneously.
Mortality versus survival in drought‐affected Aleppo pine forest depends on the extent of rock cover and soil stoniness
Authors: Preisler Yakir , Tatarinov Fyodor , Grünzweig José M. , Bert Didier , Ogée Jérôme , Wingate Lisa , Rotenberg Eyal , Rohatyn Shani , Her Nir , Moshe Itzhak , Klein Tamir , Yakir Dan 
Published: February 2019

AbstractDrought‐related tree mortality had become a widespread phenomenon in forests around the globe. This process leading to these events and its complexity is not fully understood. Trees in the dry timberline are exposed to ongoing drought, and the available water for transpiration in the soil can determine their survival chances.Recent drought years led to 5%–10% mortality in the semi‐arid pine forest of Yatir (Israel). The distribution of dead trees was, however, highly heterogeneous with parts of the forest showing >80% dead trees (D plots) and others with mostly live trees (L plots). At the tree level, visible stress was associated with low pre‐dawn leaf water potential at the dry season (−2.8 MPa vs. −2.3 MPa in non‐stressed trees), shorter needles (5.5 vs. 7.7 mm) and lower chlorophyll content (0.6 vs. 1 mg/g dw). Trends in tree‐ring widths reflected differences in stress intensity (30% narrower rings in stressed compared with unstressed trees), which could be identified 15–20 years prior to mortality.At the plot scale, no differences in topography, soil type, tree age or stand density could explain the mortality difference between the D and L plots. It could only be explained by the higher surface rock cover and in stoniness across the soil profile in the L plots. Simple bucket model simulations using the site’s long‐term hydrological data supported the idea that these differences could result in higher soil water concentration (m3/m3) in the L plots and extend the time above wilting point by several months across the long dry season.Accounting for subsurface heterogeneity may therefore critical to assessing stand‐level response to drought and projecting tree survival, and can be used in management strategies in regions undergoing drying climate trends.Aplain language summaryis available for this article.
Grassland plants show no relationship between leaf drought tolerance and soil moisture affinity, but rapidly adjust to changes in soil moisture
Authors: Májeková Maria , Martínková Jana , Hájek Tomáš 
Published: February 2019

Abstract

Assessing drought tolerance and the ability of plants to adjust to changes in available water resources is crucial for understanding current and future distributions of plant species. While turgor loss point (πtlp) has been recognized as a direct determinant of drought tolerance in woody plants, information on it for grassland species is largely missing.

We first validated a rapid method to estimate πtlp for grassland species, using osmometry measurements (πtlp‐osm) of osmotic potential at full hydration (πo‐osm), originally proposed for woody species. We confirmed that πo‐osm was tightly positively related to πtlp measured by the classic pressure–volume curve (πtlp‐pv). Cell wall elasticity was not important in the maintenance of turgor and neither specific leaf area nor leaf dry matter content influenced πtlp.

We then studied the relationship between πtlp‐osm measured under controlled conditions and species’ soil moisture affinity (Ellenberg indicator values) in 40 diverse grassland species from the full range of soil moisture conditions found in temperate grasslands. On a subset of 12 species, we studied the adjustment in πtlp‐osm to drought stress and recovery from drought.

We hypothesized that dry grassland species are better adapted to drier conditions by having comparatively higher leaf drought tolerance (more negative πtlp) and a better ability to adjust to acute drought stress.

We found that πtlp‐osm was unrelated to species’ soil moisture affinity. However, all species developed higher leaf drought tolerance by decreasing πtlp‐osm after seven weeks of drought stress. After only one week of recovery, all species reduced the leaf drought tolerance back to the πtlp‐osm level comparable with non‐stressed plants.

Our results considerably extend the relationship between πo‐osm and πtlp, originally defined for woody species, and thus propose a yet unexploited direct method for assessing leaf drought tolerance via turgor loss point in herbaceous species. However, the lack of relationship between πtlp and soil moisture affinity suggests that, unlike in woody plants, leaf‐level drought tolerance in grassland plants does not fully translate into whole‐plant drought resistance, suggesting an importance of other drought resistance strategies.

A plain language summary is available for this article.
Transparency reduces predator detection in mimetic clearwing butterflies
Authors: Arias Mónica , Mappes Johanna , Desbois Charlotte , Gordon Swanne , McClure Melanie , Elias Marianne , Nokelainen Ossi , Gomez Doris 
Published: February 2019

Abstract

Predation is an important selective pressure, and some prey have evolved conspicuous warning signals that advertise unpalatability (i.e., aposematism) as an antipredator defence. Conspicuous colour patterns have been shown effective as warning signals, by promoting predator learning and memory. Unexpectedly, some butterfly species from the unpalatable tribe Ithomiini possess transparent wings, a feature rare on land but common in water, known to reduce predator detection.

We tested whether transparency of butterfly wings was associated with decreased detectability by predators, by comparing four butterfly species exhibiting different degrees of transparency, ranging from fully opaque to largely transparent. We tested our prediction using both wild birds and humans in behavioural experiments. Vision modelling predicted butterfly detectability to be similar for these two predator types.

In concordance with predictions, the most transparent species were almost never found first and were detected less often than the opaque species by both birds and humans, suggesting that transparency enhances crypsis. However, humans were able to learn to better detect the more transparent species over time.

Our study demonstrates for the first time that transparency on land likely decreases detectability by visual predators.

A plain language summary is available for this article.
JumpDetector: An automated monitoring equipment for the locomotion of jumping insects
Authors: Zhou Feng , Kang Le , Wang Xian‐Hui 
Published: February 2019

AbstractContinuous jumping behavior, a kind of endurance locomotion, plays important roles in insect ecological adaption and survival. However, the methods used for the efficient evaluation of insect jumping behavior remain largely lacking. Here, we developed a locomotion detection system named JumpDetector with automatic trajectory tracking and data analysis to evaluate the jumping of insects. This automated system exhibits more accurate, efficient, and adjustable performance than manual methods. By using this automatic system, we characterized a gradually declining pattern of continuous jumping behavior in 4th‐instar nymphs of the migratory locust. We found that locusts in their gregarious phase outperformed locusts in their solitary phase in the endurance jumping locomotion. Therefore, the JumpDetector could be widely used in jumping behavior and endurance locomotion measurement.
Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488
Authors: Hernández‐Arriaga Ana M. , del Cerro Carlos , Urbina Leire , Eceiza Arantxa , Corcuera Mª Angeles , Retegi Aloña , Auxiliadora Prieto M. 
Published: February 2019

SummaryKomagataeibacter medellinensis ID13488 (formerly Gluconacetobacter medellinensis ID13488) is able to produce crystalline bacterial cellulose (BC) under high acidic growth conditions. These abilities make this strain desirable for industrial BC production from acidic residues (e.g. wastes generated from cider production). To explore the molecular bases of the BC biosynthesis in this bacterium, the genome has been sequenced revealing a sequence of 3.4 Mb containing three putative plasmids of 38.1 kb (pKM01), 4.3 kb (pKM02) and 3.3 Kb (pKM03). Genome comparison analyses of K. medellinensis ID13488 with other cellulose‐producing related strains resulted in the identification of the bcs genes involved in the cellulose biosynthesis. Genes arrangement and composition of four bcs clusters (bcs1, bcs2, bcs3 and bcs4) was studied by RT‐PCR, and their organization in four operons transcribed as four independent polycistronic mRNAs was determined. qRT‐PCR experiments demonstrated that mostly bcs1 and bcs4 are expressed under BC production conditions, suggesting that these operons direct the synthesis of BC. Genomic differences with the close related strain K. medellinensis NBRC 3288 unable to produce BC were also described and discussed.
Comparison of genomic landscapes of large cell neuroendocrine carcinoma, small cell lung carcinoma, and large cell carcinoma
Authors: Zhou Zhen , Zhu Lei , Niu Xiaomin , Shen Shengping , Zhao Yi , Zhang Jie , Ye Junyi , Han‐Zhang Han , Liu Junjun , Liu Chenglin , Lu Shun 
Published: February 2019

BackgroundThe classification of large cell neuroendocrine carcinoma (LCNEC) has generated considerable debate and has been revised since its recognition as a separate entity. Although it shares clinical features with small cell lung carcinoma (SCLC) and was classified with SCLC in the 2015 World Health Organization classification system, numerous studies have revealed inferior treatment outcomes of LCNEC when it was treated as SCLC. Because the incidence of LCNEC is rare, its mutational landscape has not been comprehensively interrogated.MethodsWe performed capture‐based ultra‐deep targeted sequencing on tumor samples of LCNEC, large cell carcinoma (LCC), and SCLC to elucidate its biological relationship with these subtypes and to identify potentially targetable molecular alterations.ResultsOur data revealed a molecular signature, consisting of RUNX1, ERBB4, BRCA1, and EPHA3, that is distinctively mutated in LCNEC. A majority (60%) of LCNEC patients harbored copy number variations (CNVs). Interestingly, there were no common CNVs shared among the three subtypes: NFкBIA amplification was shared between LCNEC and LCC, while AKT2 amplification was shared between LCNEC and SCLC. Furthermore, genetic alterations in the PI3K/AKT/mTOR pathway were enriched in all three subtypes.ConclusionDespite the histological and/or morphological similarities among LCNEC, LCC, and SCLC, our data revealed a molecular signature, consisting of RUNX1, ERBB4, BRCA1, and EPHA3, that is distinctively mutated in LCNEC, which has the potential to be used as a panel of biomarkers to distinguish LCNEC from a molecular perspective. Furthermore, the molecular distinction among the three subtypes can also be reflected from CNV events.
Growth of thymic epithelial tumors and thymic cysts: Differential radiological points
Authors: Kim Hyungjin , Yoon Soon Ho , Kim Jihang , Lee Kyung Won , Choi Ye Ra , Cho Hyoun , Goo Jin Mo 
Published: February 2019

BackgroundThe growth rate of thymic epithelial tumors (TETs) and thymic cysts was investigated to determine whether they can be differentiated and clinico‐radiological predictors of interval growth was identified.MethodsThis retrospective study included 122 patients with pathologically proven thymic cysts (n = 56) or TETs (n = 66) who underwent two serial chest computed tomography scans at least eight weeks apart. Average diameters and attenuation were measured, volume‐doubling times (VDTs) were calculated, and clinical characteristics were recorded. VDTs were compared using the log‐rank test. Predictors of growth were analyzed using the log‐rank test and Cox regression analysis.ResultsThe frequency of growth did not differ significantly between TETs and thymic cysts (P = 0.279). The VDT of thymic cysts (median 324 days) was not significantly different from that of the TETs (median 475 days; P = 0.808). Water attenuation (≤ 20 Hounsfield units) predicted growth in thymic cysts (P = 0.016; hazard ratio 13.2, 95% confidence interval 1.6–107.3), while lesion size (> 17.2 mm) predicted growth in TETs (P = 0.008 for size, P = 0.029 for size*time). For the growing lesions, the positive and negative predictive values of water attenuation for thymic cysts were 93% and 80%, respectively.ConclusionThe frequencies of interval growth and VDTs were indistinguishable between TETs and thymic cysts. Water attenuation and lesion size predicted growth in thymic cysts and TETs, respectively. Among the growing lesions, water attenuation was a differential feature of thymic cysts.
Age‐dependent DNA methylation patterns on the Y chromosome in elderly males
Authors: Lund Jesper B. , Li Shuxia , Christensen Kaare , Mengel‐From Jonas , Soerensen Mette , Marioni Riccardo E. , Starr John , Pattie Alison , Deary Ian J. , Baumbach Jan , Tan Qihua 
Published: February 2019

AbstractThe Y chromosome, a sex chromosome that only exists in males, has been ignored in traditional epigenetic association studies for multiple reasons. However, sex differences in aging‐related phenotypes and mortality could suggest a critical role of the sex chromosomes in the aging process. We obtained blood‐based DNA methylation data on the Y chromosome for 624 men from four cohorts and performed a chromosome‐wide epigenetic association analysis to detect Y‐linked CpGs differentially methylated over age and cross‐validated the significant CpGs in the four cohorts. We identified 40–219 significant CpG sites (false discovery rate <0.05) with >82% of them hypermethylated with increasing age, which is in strong contrast to the patterns reported on the autosomal chromosomes. Comparing the rate of change in the Y‐linked DNA methylation across cohorts that represent different age intervals revealed a trend of acceleration in DNA methylation with increasing age. The age‐dependent DNA methylation patterns on the Y chromosome were further examined for their association with all‐cause mortality with results suggesting that the predominant pattern of age‐related hypermethylation on the Y chromosome is associated with reduced risk of death.
Cannabidiol modulates the expression of neuroinflammatory factors in stress‐ and drug‐induced reinstatement of methamphetamine in extinguished rats
Authors: Karimi‐Haghighi Saeideh , Dargahi Leila , Haghparast Abbas 
Published: February 2019

AbstractMethamphetamine (METH) is a highly potent and addictive psychostimulant that is frequently abused worldwide. Although the biggest challenge to the efficient treatment of drug dependence is relapse, its mechanism is completely unclear. Plenty of evidence suggests that inflammation contributes to drug‐induced reward especially in brain regions that are involved in the reward system, but there is no document about relapse. Cannabidiol (CBD) is a nonpsychoactive cannabinoid that has powerful anti‐inflammatory and immunosuppressive properties. A previous research in our laboratory has demonstrated that CBD prevents reinstatement of METH even in 24‐hour rapid eye movement (REM) sleep‐deprived (RSD) rats. The aim of this study was to assess whether CBD prevents reinstatement of METH through change of gene expression of cytokines such as interleukin‐1β, interleukin‐6, interleukin‐10, and tumor necrosis factor α (TNF‐α) in extinguished rats. Real‐time polymerase chain reaction (PCR) was used in this research to assay gene expression of cytokines. We found that stress‐ and drug‐induced reinstatement of METH enhanced mRNA expression of cytokines in the prefrontal cortex (PFC) and hippocampus. Furthermore, CBD treatment significantly reduced the mRNA expression of cytokines in the PFC and hippocampus, but CBD treatment in RSD rats increased expression of cytokines in the hippocampus. It seems that enhancement of cytokines leads to change in neurotransmission and so triggers reinstatement of METH.
Resuscitation planning on a subacute geriatric evaluation and management ward
Authors: Strasser Rupert , Smith Roger , Yates Paul , Reid David , Katz Benny 
Published: February 2019

ObjectivesTo describe the use of acute resuscitation plans (ARPs) among patients on a subacute geriatric ward and to identify factors associated with use of ARPs in these patients.MethodsThe hospital records of all patients admitted to the geriatric medicine ward in 2016 were retrospectively audited.ResultsAn ARP was completed before separation for 333/442 (75.3%) admissions. In the event of arrest, 240 (54.3%) patients had an ARP specifying “care of the dying”, 93 (21.0%) had an ARP specifying “cardiopulmonary resuscitation” and 109 (24.7%) had no resuscitation plan. Age 85‐94 years (OR 1.65, P = 0.04) and ≥95 years (OR 9.59, P = 0.003), as well as Charlson index of comorbidity ≥2 (OR 3.4, P < 0.001), Australian‐born (OR 2.09, P = 0.002) and admission during October‐December (OR 3.81, P < 0.001) were independently associated with increased use of ARPs.ConclusionsAcute resuscitation plan use was associated with older age, higher comorbidity, birth in Australia and admission later in the year.
Lung disease in STAT3 hyper‐IgE syndrome requires intense therapy
Authors: Kröner Carolin , Neumann Jens , Ley‐Zaporozhan Julia , Hagl Beate , Meixner Iris , Spielberger Benedikt D. , Dückers Gregor , Belohradsky Bernd H. , Niehues Tim , Borte Michael , Rosenecker Joseph , Kappler Matthias , Nährig Susanne , Reu Simone , Griese Matthias , Renner Ellen D. 
Published: February 2019

AbstractBackgroundPulmonary complications are responsible for high morbidity and mortality rates in patients with the rare immunodeficiency disorder STAT3 hyper‐IgE syndrome (STAT3‐HIES). The aim of this study was to expand knowledge about lung disease in STAT3‐HIES.MethodsThe course of pulmonary disease, radiological and histopathological interrelations, therapeutic management, and the outcome of 14 STAT3‐HIES patients were assessed.ResultsThe patients’ quality of life was compromised most by pulmonary disease. All 14 patients showed first signs of lung disease at a median onset of 1.5 years of age. Lung function revealed a mixed obstructive‐restrictive impairment with reduced FEV1 and FVC in 75% of the patients. The severity of lung function impairment was associated with Aspergillus fumigatus infection and prior lung surgery. Severe lung tissue damage, with reduced numbers of ATP‐binding cassette sub‐family A member 3 (ABCA3) positive type II pneumocytes, was observed in the histological assessment of two deceased patients. Imaging studies of all patients above 6 years of age showed severe airway and parenchyma destruction. Lung surgeries frequently led to complications, including fistula formation. Long‐term antifungal and antibacterial treatment proved to be beneficial, as were inhalation therapy, chest physiotherapy, and exercise. Regular immunoglobulin replacement therapy tended to stabilize lung function.ConclusionsDue to its severity, pulmonary disease in STAT3‐HIES patients requires strict monitoring and intensive therapy.
Reliability of frailty assessment in the critically ill: a multicentre prospective observational study
Authors: Pugh R. J. , Battle C. E. , Thorpe C. , Lynch C. , Williams J. P. , Campbell A. , Subbe C. P. , Whitaker R. , Szakmany T. , Clegg A. P. , Lone N. I. 
Published: February 2019

SummaryDemand for critical care among older patients is increasing in many countries. Assessment of frailty may inform discussions and decision making, but acute illness and reliance on proxies for history‐taking pose particular challenges in patients who are critically ill. Our aim was to investigate the inter‐rater reliability of the Clinical Frailty Scale for assessing frailty in patients admitted to critical care. We conducted a prospective, multi‐centre study comparing assessments of frailty by staff from medical, nursing and physiotherapy backgrounds. Each assessment was made independently by two assessors after review of clinical notes and interview with an individual who maintained close contact with the patient. Frailty was defined as a Clinical Frailty Scale rating > 4. We made 202 assessments in 101 patients (median (IQR [range]) age 69 (65–75 [60–80]) years, median (IQR [range]) Acute Physiology and Chronic Health Evaluation II score 19 (15–23 [7–33])). Fifty‐two (51%) of the included patients were able to participate in the interview; 35 patients (35%) were considered frail. Linear weighted kappa was 0.74 (95%CI 0.67–0.80) indicating a good level of agreement between assessors. However, frailty rating differed by at least one category in 47 (47%) cases. Factors independently associated with higher frailty ratings were: female sex; higher Acute Physiology and Chronic Health Evaluation II score; higher category of pre‐hospital dependence; and the assessor having a medical background. We identified a good level of agreement in frailty assessment using the Clinical Frailty Scale, supporting its use in clinical care, but identified factors independently associated with higher ratings which could indicate personal bias.