bluuebunny/crossref_metadata_2025_split huggingface dataset:
LLPSDB: a database of proteins undergoing liquid–liquid phase separation in vitro
Authors: Li Qian , Peng Xiaojun , Li Yuanqing , Tang Wenqin , Zhu Jia’an , Huang Jing , Qi Yifei , Zhang Zhuqing 
Published: August 2019

Abstract
Liquid-liquid phase separation (LLPS) leads to a conversion of homogeneous solution into a dense phase that often resembles liquid droplets, and a dilute phase. An increasing number of investigations have shown that biomolecular condensates formed by LLPS play important roles in both physiology and pathology. It has been suggested the phase behavior of proteins would be not only determined by sequences, but controlled by micro-environmental conditions. Here, we introduce LLPSDB (http://bio-comp.ucas.ac.cn/llpsdb or http://bio-comp.org.cn/llpsdb), a web-accessible database providing comprehensive, carefully curated collection of proteins involved in LLPS as well as corresponding experimental conditions in vitro from published literatures. The current release of LLPSDB incorporates 1182 entries with 273 independent proteins and 2394 specific conditions. The database provides a variety of data including biomolecular information (protein sequence, protein modification, nucleic acid, etc.), specific phase separation information (experimental conditions, phase behavior description, etc.) and comprehensive annotations. To our knowledge, LLPSDB is the first available database designed for LLPS related proteins specifically. It offers plenty of valuable resources for exploring the relationship between protein sequence and phase behavior, and will enhance the development of phase separation prediction methods, which may further provide more insights into a comprehensive understanding of LLPS in cellular function and related diseases.
Simultaneous targeting of DNA replication and homologous recombination in glioblastoma with a polyether ionophore
Authors: Lim Yi Chieh , Ensbey Kathleen S , Offenhäuser Carolin , D’souza Rochelle C J , Cullen Jason K , Stringer Brett W , Quek Hazel , Bruce Zara C , Kijas Amanda , Cianfanelli Valentina , Mahboubi Bijan , Smith Fiona , Jeffree Rosalind L , Wiesmüeller Lisa , Wiegmans Adrian P , Bain Amanda , Lombard Fanny J , Roberts Tara L , Khanna Kum Kum , Lavin Martin F , Kim Baek , Hamerlik Petra , Johns Terrance G , Coster Mark J , Boyd Andrew W , Day Bryan W 
Published: August 2019

Abstract

Background
Despite significant endeavor having been applied to identify effective therapies to treat glioblastoma (GBM), survival outcomes remain intractable. The greatest nonsurgical benefit arises from radiotherapy, though tumors typically recur due to robust DNA repair. Patients could therefore benefit from therapies with the potential to prevent DNA repair and synergize with radiotherapy. In this work, we investigated the potential of salinomycin to enhance radiotherapy and further uncover novel dual functions of this ionophore to induce DNA damage and prevent repair.

Methods
In vitro primary GBM models and ex vivo GBM patient explants were used to determine the mechanism of action of salinomycin by immunoblot, flow cytometry, immunofluorescence, immunohistochemistry, and mass spectrometry. In vivo efficacy studies were performed using orthotopic GBM animal xenograft models. Salinomycin derivatives were synthesized to increase drug efficacy and explore structure-activity relationships.

Results
Here we report novel dual functions of salinomycin. Salinomycin induces toxic DNA lesions and prevents subsequent recovery by targeting homologous recombination (HR) repair. Salinomycin appears to target the more radioresistant GBM stem cell–like population and synergizes with radiotherapy to significantly delay tumor formation in vivo. We further developed salinomycin derivatives which display greater efficacy in vivo while retaining the same beneficial mechanisms of action.

Conclusion
Our findings highlight the potential of salinomycin to induce DNA lesions and inhibit HR to greatly enhance the effect of radiotherapy. Importantly, first-generation salinomycin derivatives display greater efficacy and may pave the way for clinical testing of these agents.
The Presence and Persistence of Unrealistic Expectations in Patients Undergoing Nerve Surgery
Authors: Kirsch Michael , Brown Shawn , Smith Brandon W , Chang Kate W C , Koduri Sravanthi , Yang Lynda J S 
Published: August 2019

Abstract

BACKGROUND
Unrealistic expectations of the outcomes of peripheral nerve surgery reduce patient satisfaction. Most clinicians can recall patients with unrealistic expectations despite verbal preoperative education.

OBJECTIVE
To assess patients’ baseline level of understanding regarding nerve surgery and appropriate expectations. Additionally, we tested the effect of a written, preoperative educational handout on the patients’ retention of knowledge.

METHODS
This cross-sectional survey recruited patients scheduled to undergo peripheral nerve surgery at a single institution in 2016 to 2017. During the preoperative visit, a specialized nurse practitioner reviewed perioperative protocols, risks and benefits of the surgery, and postoperative care. Patients immediately completed a survey to assess their preoperative understanding of the verbally reviewed information. During the same visit, an additional written handout was given to patients in a randomized fashion. At their first postoperative visit, all patients completed the survey again.

RESULTS
A total of 60 patients (mean age 52 yr) were enrolled of which 62% were male. Immediately following verbal instruction, 31% of patients had erroneous (unrealistic) expectations regarding pain, 30% had erroneous expectations regarding postoperative motor outcome, and 41% had erroneous expectations regarding the timing of postoperative recovery. There was no significant difference between patients who received the written handout vs those who did not, on retesting in the postoperative period.

CONCLUSION
Patients undergoing peripheral nerve procedures demonstrated a high baseline level of unrealistic expectations despite standard in-person verbal counseling by specialty providers. A written handout did not have clear benefit in the retention of preoperative surgical teaching. Further investigation into more effective preoperative patient counseling is needed.
The Safety and Feasibility of Mechanical Thrombectomy for Mild Acute Ischemic Stroke With Large Vessel Occlusion
Authors: Toth Gabor , Ortega-Gutierrez Santiago , Tsai Jenny P , Cerejo Russell , Al Kasab Sami , Uchino Ken , Hussain M Shazam , Bain Mark , Bullen Jennifer , Samaniego Edgar A 
Published: August 2019

Abstract

BACKGROUND
Prospective evidence to support mechanical thrombectomy (MT) for mild ischemic stroke with large vessel occlusion (LVO) is lacking. There is uncertainty about using an invasive procedure in patients with mild symptoms.

OBJECTIVE
To evaluate the safety and feasibility of MT in patients with mild symptoms and LVO.

METHODS
Our single-arm prospective pilot study recruited patients with LVO and initial National Institute of Health Stroke Scale (NIHSS) <6, who underwent standard MT. Primary safety endpoints were symptomatic intracerebral hemorrhage (sICH), and/or worsening NIHSS by ≥4 points. Secondary endpoints included angiographic recanalization, NIHSS change, final infarct volume, and modified Rankin score (mRS).

RESULTS
We enrolled 20 patients (mean age 65.6 ± 12.3 yr; 45% females). Thrombolysis in Cerebral Ischemia 2B/3 thrombectomy was achieved in 95%. No patients suffered sICH. One patient (5%) had neurologic worsening within 24 h because of underlying intracranial stenosis. No other complications or safety concerns were identified. Median NIHSS was significantly better at discharge (0.5, P = .007) and at last follow-up (0, P < .001) than before treatment (3). Mean post vs preintervention infarct volumes were small without significant difference (1.2 ml, P = .434). Most patients (85%) were discharged directly home. Excellent clinical outcome (mRS 0-1) at last follow-up was seen in 95% of patients.

CONCLUSION
This is one of the first specifically designed prospective studies showing that MT is safe and feasible in patients with low NIHSS and LVO. Chronic underlying vasculopathy may be a challenging dilemma. We observed excellent clinical and radiographic outcomes, but randomized controlled trials are needed to demonstrate the efficacy of MT in this unique cohort.
Marketing Influences on Perceptions of Reduced Nicotine Content Cigarettes
Authors: Johnson Andrea C , Mays Darren , Villanti Andrea C , Niaura Raymond S , Rehberg Kathryn , Phan Lilianna , Mercincavage Melissa , Luta George , Strasser Andrew A 
Published: August 2019

Abstract

Introduction
The Food and Drug Administration announced intent to reduce the nicotine content in cigarettes. There is limited evidence on how reduced nicotine content cigarette (RNC) marketing affects product beliefs and use, and research on this is needed to inform regulations.

Methods
In an online experiment, 426 young adult cigarette smokers (aged 18–30 years) were randomized in a 2 (implicit: red package vs. blue package) × 2 (explicit: corrective message vs. no corrective message) design to view an advertisement for previously commercially available RNCs. Outcomes were advertisement content recall, product beliefs, and use intentions. Participants’ responses to open-ended assessment of their beliefs about the stimuli were coded to identify prevailing themes.

Results
Red packaging and corrective messaging were independently associated with greater advertisement content recall (p = .01 and p = .04, respectively). There were no significant main or interaction effects on product beliefs or use intentions. Controlling for condition, advertisement content recall was significantly associated with less favorable product beliefs (p &lt; .001) and favorable product beliefs were associated with intent to use the product (p &lt; .001). Open-ended responses converged on the finding that respondents were interested in RNCs, but expressed skepticism about effectiveness and value.

Conclusions
Brief exposure to an RNC advertisement with red packaging and corrective messaging were each independently associated with greater advertisement content recall. The results indicate: (1) interest and confusion among young adult smokers regarding RNCs, (2) beliefs about RNCs are influenced by marketing, and (3) beliefs are associated with intention to use RNCs.

Implications
Findings from this study demonstrate the importance of advertising effects on beliefs about RNC products and support the need to regulate advertising and labeling alongside product regulation. More detailed study of advertisement features that affect consumers’ beliefs about RNCs and how they impact their processing of explicit messaging about product risks will be important to guide regulatory decision-making.
Predicting Improved Daily Use of the More Affected Arm Poststroke Following Constraint-Induced Movement Therapy
Authors: Rafiei Mohammad H , Kelly Kristina M , Borstad Alexandra L , Adeli Hojjat , Gauthier Lynne V 
Published: August 2019

Abstract

Background
Constraint-induced movement therapy (CI therapy) produces, on average, large and clinically meaningful improvements in the daily use of a more affected upper extremity in individuals with hemiparesis. However, individual responses vary widely.

Objective
The study objective was to investigate the extent to which individual characteristics before treatment predict improved use of the more affected arm following CI therapy.

Design
This study was a retrospective analysis of 47 people who had chronic (&gt; 6 months) mild to moderate upper extremity hemiparesis and were consecutively enrolled in 2 CI therapy randomized controlled trials.

Methods
An enhanced probabilistic neural network model predicted whether individuals showed a low, medium, or high response to CI therapy, as measured with the Motor Activity Log, on the basis of the following baseline assessments: Wolf Motor Function Test, Semmes-Weinstein Monofilament Test of touch threshold, Motor Activity Log, and Montreal Cognitive Assessment. Then, a neural dynamic classification algorithm was applied to improve prognostic accuracy using the most accurate combination obtained in the previous step.

Results
Motor ability and tactile sense predicted improvement in arm use for daily activities following intensive upper extremity rehabilitation with an accuracy of nearly 100%. Complex patterns of interaction among these predictors were observed.

Limitations
The fact that this study was a retrospective analysis with a moderate sample size was a limitation.

Conclusions
Advanced machine learning/classification algorithms produce more accurate personalized predictions of rehabilitation outcomes than commonly used general linear models.
Improving the feasibility of MRI in clinically suspect arthralgia for prediction of rheumatoid arthritis by omitting scanning of the feet
Authors: Boer Aleid C , Wouters Fenne , Dakkak Yousra J , Niemantsverdriet Ellis , van der Helm-van Mil Annette H M 
Published: August 2019

Abstract

Objectives
The use of MR-imaging is recommended for the early detection of RA. Next to the small joints of the hands, foot-joints are often involved. Therefore, imaging inflammation of the feet in addition to hands may be informative, but prolongs scan-time and leads to additional costs. We studied the value of MRI of the feet alone and complementary to MRI of the hands in patients with clinically suspect arthralgia (CSA).

Methods
357 consecutively included CSA patients underwent contrast-enhanced 1.5 T-MRI of hand (MCP2-5 and wrist) and foot (MTP1-5) joints at baseline. Scans were scored for synovitis, osteitis and tenosynovitis. After ⩾1 year follow-up, the development of clinically apparent inflammatory arthritis (IA) was studied. Cox regression was performed and test characteristics were evaluated. Sensitivity analyses were performed for the outcome RA-development (2010-criteria).

Results
MRI-detected tenosynovitis of the feet was associated with IA-development, independently from synovitis and osteitis hazard ratio (HR) (95%CI) 4.75 (2.38; 9.49), and independently from ACPA and CRP, HR 3.13 (1.48; 6.64). From all CSA patients, 11% had inflammation in hands and feet, 29% only in hands and 3% only in feet. In line with this finding, the addition of MRI-feet to MRI-hands did not increase the predictive accuracy; the sensitivity remained 77%, while the specificity decreased from 66% to 62%. Sensitivity analyses with RA development as outcome showed similar results.

Conclusion
Tenosynovitis at the forefeet in CSA predicted IA and RA development. Addition of foot MRI to hand MRI did not increase the accuracy. Foot MRI can be omitted to reduce scan time and costs and increase the feasibility.
Accurate Inference of Tree Topologies from Multiple Sequence Alignments Using Deep Learning
Authors: Suvorov Anton , Hochuli Joshua , Schrider Daniel R 
Published: August 2019

Abstract
Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several “zones” of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. In this study, we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate on simulated data, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. Although numerous practical challenges remain, these findings suggest that the deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.
Tracking the route of atmospheric nitrogen to diazotrophs colonizing buried mangrove roots
Authors: Inoue Tomomi , Kohzu Ayato , Shimono Ayako 
Published: August 2019

Abstract
Nitrogen-fixing activity has been observed in the rhizosphere of mangrove ecosystems, suggesting a close mangrove–diazotroph relationship. In regularly flooded soil, however, the pathway by which atmospheric nitrogen reaches the diazotrophs in the rhizosphere is unknown. This study provides evidence that mangrove aerial roots serve as pathways that supply nitrogen gas to the diazotrophs colonizing buried roots. A plastic chamber was attached on the exposed part of a Rhizophora stylosa Griff prop root, and 15N2 tracer gas was injected into it. The entire root, including the below-ground part, was collected for analysis of 15N labelling and nitrogenase activity. We detected 15N labelling in buried root materials 2 h after gas injection. Compared with the δ15N contents in root material from an untreated tree, the increment was &gt;10‰ in lateral roots. The nitrogenase activity measured on the other R. stylosa roots was highest in lateral roots, matching well with the results of 15N labelling. Our results indicate that atmospheric nitrogen is taken into aerial mangrove roots through lenticels, diffuses into the buried root system and is fixed by diazotrophs. The unusual appearance of mangrove aerial roots, which has intrigued researchers for many years, could be a key to the high productivity of mangrove ecosystems.
Genetic differentiation in functional traits among European sessile oak populations
Authors: Torres-Ruiz José M , Kremer Antoine , Carins Murphy Madeline R , Brodribb Tim , Lamarque Laurent J , Truffaut Laura , Bonne Fabrice , Ducousso Alexis , Delzon Sylvain 
Published: August 2019

AbstractThe vulnerability of forest species and tree populations to climate change is related to the exposure of the ecosystem to extreme climatic conditions and to the adaptive capacity of the population to cope with those conditions. Adaptive capacity is a relatively under-researched topic within the forest science community, and there is an urgent need to understand to what extent particular combinations of traits have been shaped by natural selection under climatic gradients, potentially resulting in adaptive multi-trait associations. Thus, our aim was to quantify genetic variation in several leaf and woody traits that may contribute to multi-trait associations in which intra-specific variation could represent a source for species adaptation to climate change. A multi-trait approach was performed using nine Quercus petraea provenances originating from different locations that cover most of the species’ distribution range over Europe and that were grown in a common garden. Multiple adaptive differences were observed between oak provenances but also some evolutionary stasis. In addition, our results revealed higher genetic differentiation in traits related to phenology and growth than in those related to xylem anatomy, physiology and hydraulics, for which no genetic differentiation was observed. The multiple associations between those traits and climate variables resulting from multivariate and path analyses suggest a multi-trait association largely involving phenological and growth traits for Q. petraea.
Embolism resistance of different aged stems of a California oak species (Quercus douglasii): optical and microCT methods differ from the benchtop-dehydration standard
Authors: Pratt R Brandon , Castro Viridiana , Fickle Jaycie C , Jacobsen Anna L 
Published: August 2019

AbstractVulnerability of xylem to embolism is an important trait related to drought resistance of plants. Methods continue to be developed and debated for measuring embolism. We tested three methods (benchtop dehydration/hydraulic, micro-computed tomography (microCT) and optical) for assessing the vulnerability to embolism of a native California oak species (Quercus douglasii Hook. & Arn.), including an analysis of three different stem ages. All three methods were found to significantly differ in their estimates, with a greater resistance to embolism as follows: microCT &gt; optical &gt; hydraulic. Careful testing was conducted for the hydraulic method to evaluate multiple known potential artifacts, and none was found. One-year-old stems were more resistant than older stems using microCT and optical methods, but not hydraulic methods. Divergence between the microCT and optical methods from the standard hydraulic method was consistent with predictions based on known errors when estimating theoretical losses in hydraulic function in both microCT and optical methods. When the goal of a study is to describe or predict losses in hydraulic conductivity, neither the microCT nor optical methods are reliable for accurately constructing vulnerability curves of stems; nevertheless, these methods may be useful if the goal of a study is to identify embolism events irrespective of hydraulic conductivity or hydraulic function.
Effects of elevated carbon dioxide and elevated temperature on morphological, physiological and anatomical responses of Eucalyptus tereticornis along a soil phosphorus gradient
Authors: Duan Honglang , Ontedhu Josephine , Milham Paul , Lewis James D , Tissue David T 
Published: August 2019

AbstractEucalypts are likely to play a critical role in the response of Australian forests to rising atmospheric CO2 concentration ([CO2]) and temperature. Although eucalypts are frequently phosphorus (P) limited in native soils, few studies have examined the main and interactive effects of P availability, [CO2] and temperature on eucalypt morphology, physiology and anatomy. To address this issue, we grew seedlings of Eucalyptus tereticornis Smith across its P-responsive range (6–500 mg kg−1) for 120 days under two [CO2] (ambient: 400 μmol mol−1 (Ca) and elevated: 640 μmol mol−1 (Ce)) and two temperature (ambient: 24/16 °C (Ta) and elevated: 28/20 °C (Te) day/night) treatments in a sunlit glasshouse. Seedlings were well-watered and supplied with otherwise non-limiting macro- and micro-nutrients. Increasing soil P supply increased growth responses to Ce and Te. At the highest P supplies, Ce increased total dry mass, leaf number and total leaf area by ~50%, and Te increased leaf number by ~40%. By contrast, Ce and Te had limited effects on seedling growth at the lowest P supply. Soil P supply did not consistently modify photosynthetic responses to Ce or Te. Overall, effects of Ce and Te on growth, physiological and anatomical responses of E. tereticornis seedlings were generally neutral or negative at low soil P supply, suggesting that native tree responses to future climates may be relatively small in native low-P soils in Australian forests.