bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unified field studies of the algae testbed public-private partnership as the benchmark for algae agronomics
Authors: Knoshaug Eric P. , Wolfrum Ed , Laurens Lieve M. L. , Harmon Valerie L. , Dempster Thomas A. , McGowen John 
Published: November 2018

AbstractNational scale agronomic projections are an important input for assessing potential benefits of algae cultivation on the future of innovative agriculture. The Algae Testbed Public-Private Partnership was established with the goal of investigating open pond algae cultivation across different geographic, climatic, seasonal, and operational conditions while setting the benchmark for quality data collection, analysis, and dissemination. Identical algae cultivation systems and data analysis methodologies were established at testbed sites across the continental United States and Hawaii. Within this framework, the Unified Field Studies were designed for algae cultivation during all 4 seasons across the testbed network. With increasingly diverse algae research and development, and field deployment strategies, the challenges associated with data collection, quality, and dissemination increase dramatically. The dataset presented here is the complete, curated, climatic, cultivation, harvest, and biomass composition data for each season at each site. These data enable others to do in-depth cultivation, harvest, techno-economic, life cycle, resource, and predictive growth modelling analysis, as well as development of crop protection strategies throughout the algae cultivation industry.
Phosphofructokinase controls the acetaldehyde-induced phase shift in isolated yeast glycolytic oscillators
Authors: van Niekerk David D. , Gustavsson Anna-Karin , Mojica-Benavides Martin , Adiels Caroline B. , Goksör Mattias , Snoep Jacky L. 
Published: November 2018

Abstract
The response of oscillatory systems to external perturbations is crucial for emergent properties such as synchronisation and phase locking and can be quantified in a phase response curve (PRC). In individual, oscillating yeast cells, we characterised experimentally the phase response of glycolytic oscillations for external acetaldehyde pulses and followed the transduction of the perturbation through the system. Subsequently, we analysed the control of the relevant system components in a detailed mechanistic model. The observed responses are interpreted in terms of the functional coupling and regulation in the reaction network. We find that our model quantitatively predicts the phase-dependent phase shift observed in the experimental data. The phase shift is in agreement with an adaptation leading to synchronisation with an external signal. Our model analysis establishes that phosphofructokinase plays a key role in the phase shift dynamics as shown in the PRC and adaptation time to external perturbations. Specific mechanism-based interventions, made possible through such analyses of detailed models, can improve upon standard trial and error methods, e.g. melatonin supplementation to overcome jet-lag, which are error-prone, specifically, since the effects are phase dependent and dose dependent. The models by Gustavsson and Goldbeter discussed in the text can be obtained from the JWS Online simulation database: (https://jjj.bio.vu.nl/models/gustavsson5 and https://jjj.bio.vu.nl/models/goldbeter1)
Ultra‐low light reflection surface using metal‐coated high‐aspect‐ratio nanopillars
Authors: Jung Ju Ho , Han Eui Don , Kim Byeong Hee , Seo Young Ho , Park Yong Min 
Published: November 2018

The study investigated the anti‐reflective properties of metal‐coated nanopillar arrays with high‐aspect ratio. Aluminium oxyhydroxide nanopillar arrays were prepared by using aluminium anodic oxidation, hydrothermal synthesis, and platinum sputtering on their surface. The anti‐reflective properties were evaluated on four types of nanostructures such as nanolens and nanopillar arrays with aspect ratios of 1:0.5, 1:3, 1:9, and 1:14. The nanopillar arrays with an aspect ratio of 1:14 demonstrated extremely low reflectance <0.18% at 550 nm wavelength of all measured incident angles.
Posterior versus direct anterior approach in total hip arthroplasty: difference in patient-reported outcomes measured with the Forgotten Joint Score-12
Authors: Ozaki Yu , Baba Tomonori , Homma Yasuhiro , Ochi Hironori , Watari Taiji , Banno Sammy , Matsumoto Mikio , Kaneko Kazuo 
Published: November 2018

Introduction: When the postoperative outcome of primary total hip arthroplasty (THA) was compared with the direct anterior approach (DAA) and the posterior approach (PA), there was no significant difference of the clinical outcome at 6 months to 1 year after surgery in many studies. This study was performed to compare the medium-term outcome of THA via the DAA or PA and clarify which approach achieves better quality of life (QOL).Methods: We investigated 61 hips receiving primary THA (30 via DAA and 31 via PA), using hip function scores such as the Harris Hip Score (HHS) and patient-reported outcomes such as the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), the Japanese Orthopaedic Association Hip Disease Evaluation Questionnaire (JHEQ), and the Forgotten Joint Score-12 (FJS).Results: The mean duration of postoperative follow-up was 36.8 months in the DAA group and 40.5 months in the PA group. There was no difference in preoperative or postoperative HHS between the two groups. Although there was no difference of postoperative WOMAC and JHEQ, the postoperative FJS-12 score was significantly higher in the DAA group than in the PA group (75.2 ± 15.9 versus 60.1 ± 24.4,p = 0.01).Conclusion: When forgetting the artificial joint in daily life is the target, better QOL can be achieved by performing THA via the DAA.
Debora: Akzeptanz und Machbarkeit eines Schmerzkompetenz- und Depressionspräventionstrainings in der VMO
Authors: Korsch Sabrina , Köpnick Anne , Hampel Petra 
Published: November 2018

Zusammenfassung
Ziel der Studie Es herrscht ein zunehmender Bedarf an der Etablierung von Patientenschulungen bei chronischem Rückenschmerz und psychischer Komorbidität. Die vorliegende Studie fand im Setting der stationären verhaltensmedizinisch orthopädischen Rehabilitation (VMO) statt und untersuchte die Akzeptanz und Machbarkeit des kombinierten Schmerzkompetenz- und Depressionspräventionstrainings Debora im Vergleich von Interventions- zur Kontrollgruppe. Während die Interventionsgruppe das kombinierte kognitiv-behaviorale Training erhielt, nahmen Rehabilitanden der Kontrollgruppe lediglich am Schmerzkompetenztraining teil.
Methodik Insgesamt wurden 3 Teilstudien für die formative Evaluation herangezogen. Das triangulative Design setzte sich aus problemzentrierten Interviews und Fokusgruppen mit Rehabilitanden sowie Fokusgruppen mit Experten zusammen. Die Interviews wurden transkribiert, anonymisiert und anschließend inhaltsanalytisch ausgewertet.
Ergebnisse Sowohl aus Rehabilitanden- als auch aus Expertenperspektive lag eine gute Akzeptanz und Machbarkeit des Trainings vor. Die durchführenden Therapeuten hatten bedeutsamen Einfluss auf die Teilnehmerzufriedenheit. Verbesserungswünsche gab es hauptsächlich zum Ausbau von Inhalten zur Schmerz- und Stressbewältigung sowie hinsichtlich der Beratung der individuellen Problemlagen. Die Kontrollgruppe bewertete das Training, unabhängig von der Depressivität, insgesamt schlechter und wies verglichen mit der Interventionsgruppe eine schlechtere Gruppenkohärenz auf.
Schlussfolgerung Die Ergebnisse der formativen Evaluation sprechen für die kombinierte Durchführung des Schmerzkompetenz- und Depressionspräventionstrainings Debora und legen die langfristige Etablierung des Trainings in der stationären VMO nahe.
An Opinion Survey of Orthopaedic and Traumatology Surgeons Working in Outpatient Care (Society, Laws and Patients)
Authors: Omari Ehsan , Thoma Wolfgang , Schulze Johannes 
Published: November 2018

Abstract
Background The German health care system is well accepted, but efficiency, costs and patient satisfaction are sometimes criticised. Opinions and models prevail, and empirical data are rarely presented, although quantitative data are a precondition to assess the acceptance of the health care system.
Method To determine the appraisal of the patient-doctor relationship, economic situation and cooperation with clinical institutions, a 37 item was developed where participants indicated their agreement with a statement on a four point Likert scale. This questionnaire was answered by 525 German orthopaedic and/or traumatology surgeons, representing 7.7% of all German specialists working in outpatient care.
Results 75% of all respondents felt challenged by demanding patients and a need for justification; what was less pronounced was the feeling of being exploited as physicians. Restrictions in medical treatment from budgeting expenses were seen by 74%. More than 90% considered that it was impossible to finance their medical practice expenses by conservative medical treatment only. The respondents felt similarly critical about the current cooperation with hospitals – only 19% were not interested in closer cooperation and 96% advocated higher fees for this cooperation. 74% confirmed that hospitals are taking over outpatient tasks, whereas only 35% agreed that more clinical patient care can be provided by outpatient providers, especially due to legal restrictions.
Discussion Practitioning orthopaedic and traumatology surgeons feel exploited by uninformed patients, misallocation of reimbursement funds and legal restrictions, as well as unilateral substitution of outpatient care by hospitals. They do not consider that the current structures are sustainable for long term patient care.
Body Composition and Strength Parameters in Elite Judo Athletes 5 Years after Anterior Cruciate Ligament Reconstruction
Authors: Prill Robert , Michel Sven , Schulz Robert , Coriolano Hans-Joachim 
Published: November 2018

AbstractThe purpose of this study was to investigate if there are still deficits in muscle mass or strength capabilities in elite judo athletes with a history of anterior cruciate ligament reconstruction (ACLR) after their return to the sport. Therefore, bioimpedance analysis, 3D-laser thigh circumference measurement and isokinetic dynamometry in a closed kinetic chain were used. The side-to-side differences were investigated in a group of judo athletes 5 years after ACLR (n=17) and compared with a group of healthy judo athletes (n=27). Neither thigh circumferences, nor muscle masses of the lower extremities differed in formerly injured judo athletes compared to healthy judo athletes. In contrast, isokinetic strength testing showed a significantly larger side-to-side difference of peak muscle force in formerly injured judo athletes (p=0.021). They provided significantly lower peak forces with the formerly injured leg than with the non-injured leg (p<0.001). The authors conclude that strength capabilities, but not body composition, remains altered in recovered judo athletes in mean 5 years after ACLR and definitely after their return to sports. This indicates that the focus of rehabilitation protocols and return to sports assessments should focus more on maximum strength capabilities.
Retrospective Analysis of Whole-Body Magnetic Resonance Imaging of Bone Manifestations in Long-Term Treated Patients with Gaucher Disease Type 1
Authors: Lollert André , Laudemann Katharina , Mengel Eugen , Hoffmann Christian , Moos Larissa , Reinke Jörg , Brixius-Huth Miriam , Hennermann Julia , Düber Christoph , Staatz Gundula 
Published: November 2018

Abstract
Purpose We retrospectively assessed bone and visceral manifestations in patients with Gaucher disease type 1 (GD1) with whole-body magnetic resonance imaging (WB-MRI) to determine the effects of different timing in initiating long-term enzyme replacement therapy.
Materials and Methods In 17 patients with GD1, we performed 2 WB-MRI examinations at a median interval of 13 months. Patients had received enzyme replacement therapy with alglucerase/imiglucerase for a median of 13 years prior to the first examination. MRI results were retrospectively stratified based on treatment initiation into 2 groups: “early” (age ≤12 years, median 5 years) and “late” (during adulthood, median 32 years). We evaluated occurrence of irreversible avascular necroses (AVN) and applied several semi-quantitative scores, including the Bone-Marrow-Burden (BMB) score, the Düsseldorf-Gaucher score (DGS), the Vertebra-Disc-Ratio (VDR), and the Gaucher disease type 1 Severity Scoring System (GD-DS3).
Results MRI assessments showed no AVN in the “early” group. AVN were observed in 2 patients of the “late” group; one also had a splenic Gaucheroma. The follow-up examinations showed slight improvements in the BMB-score, DGS, and VDR, with similar tendencies in both treatment groups. The GD-DS3 score only improved in “late” group.
Conclusion This retrospective study supported the ongoing clinical value of enzyme replacement therapy with alglucerase/imiglucerase, as WB-MRI-based scores stayed constant or slightly improved even after long-term treatment. Secondary complications were only observed in the late treatment group. Our results suggest that “early initiation” of enzyme replacement therapy may protect the bone.
Lemierre Syndrome: Clinical Update and Protocol for a Systematic Review and Individual Patient Data Meta-analysis
Authors: Sacco Clara , Zane Federica , Granziera Serena , Holm Karin , Creemers-Schild Dina , Hotz Michel-André , Turpini Elena , Valentini Adele , Righini Christian , Karkos Petros , Verhamme Peter , Di Nisio Marcello , Konstantinides Stavros , Pecci Alessandro , Barco Stefano ,   on behalf of the Lemierre Study Group
Published: November 2018

AbstractLemierre syndrome usually affects otherwise healthy adolescents or young adults and occurs at an overall rate of 1 to 10 cases per million person-years with an estimated fatality rate of 4 to 9%. Diagnostic criteria remain debated and include acute neck/head bacterial infection (often tonsillitis caused by anaerobes at high potential for sepsis and vascular invasion, notably Fusobacterium necrophorum) complicated by local vein thrombosis, usually involving the internal jugular vein, and systemic septic embolism. Medical treatment is based on antibiotic therapy with anaerobic coverage, anticoagulant drugs and supportive care in case of sepsis. Surgical procedures can be required, including drainage of the abscesses, tissue debridement and jugular vein ligation. Evidence for clinical management is extremely poor in the absence of any adequately sized study with clinical outcomes. In this article, we illustrate two cases of Lemierre syndrome not caused by Fusobacterium necrophorum and provide a clinically oriented discussion on the main issues on epidemiology, pathophysiology and management strategies of this disorder. Finally, we summarize the study protocol of a proposed systematic review and individual patient data meta-analysis of the literature. Our ongoing work aims to investigate the risk of new thromboembolic events, major bleeding or death in patients diagnosed with Lemierre syndrome, and to better elucidate the role of anticoagulant therapy in this setting. This effort represents the starting point for an evidence-based treatment of Lemierre syndrome built on multinational interdisciplinary collaborative studies.
The Mutual Relation of Platelet Activation and Innate Immunity
Authors: Eisinger Felix , Langer Harald 
Published: November 2018

AbstractPlatelets are known to be central regulators of haemostasis, inflammation and immune response. Formed by megakaryocytes in the bone marrow and the lungs, platelets express a broad range of adhesion receptors and release cytokines and platelet microparticles which enable them to interact with both immune cells and pathogens. In bacterial and viral infections, thrombophilia and thrombocytopenia are commonly seen symptoms, indicating the close relationship between haemostasis and immune defence. Indeed, platelets contribute both directly and via immune mediation to pathogen clearance. In sterile inflammation, a pathogen-free process which is often triggered by cell necrosis and autoimmune reactions, platelets are also of central importance. Recently, platelet inflammasome has been extensively studied in this context. Both sterile inflammation and infection are affected by the interactions of platelets and innate immunity, notably the complement system. Although the general elements of this interplay have been known for long, more and more insights into disease-specific mechanisms could be gained recently. This review gives an outline of the current findings in the field of platelet–immune cell interactions and points out possible implications for clinical therapy.
Future Antithrombotic Therapies in Cardiology
Authors: Bäuml Marina , Hilgendorf Ingo 
Published: November 2018

AbstractThrombi are composed of activated platelets and fibrin, the latter being the final product of the blood coagulation system. Therefore, antithrombotic therapies may either interfere with adhesion, aggregation, secretion or signalling of platelets or with fibrin formation. Established drugs potently inhibit clot formation, but also increase the risk of bleeding. In this review article, we discuss novel strategies for the inhibition of pathological thrombosis while enabling normal haemostasis, thus minimizing the risk of bleeding.
Aortomegaly Causing Nutcracker Syndrome and Pelvic Congestion Syndrome
Authors: Rathod Krantikumar , Sahu Amit , Popat Bhavesh , Deshmukh Hemant 
Published: November 2018

AbstractThe authors present an uncommon cause of pelvic congestion syndrome (PCS) secondary to anterior nutcracker syndrome, which was caused by aortomegaly. Positional flank and pelvic pain was the only presenting feature with no renal dysfunction. Early and significant decompression of left renal vein (LRV) via left ovarian vein resulted in preserved renal function with symptomatic pelvic varices. Endovascular management by left ovarian vein coiling and LRV stenting was done. They briefly review the etiopathology, imaging, treatment rationale, and management options for nutcracker and PCS.
Metabolic network-based stratification of hepatocellular carcinoma reveals three distinct tumor subtypes
Authors: Bidkhori Gholamreza , Benfeitas Rui , Klevstig Martina , Zhang Cheng , Nielsen Jens , Uhlen Mathias , Boren Jan , Mardinoglu Adil 
Published: November 2018

Significance
Hepatocellular carcinoma (HCC) is a heterogeneous and deadly form of liver cancer. Here, we stratified and characterized HCC tumors by applying graph and control theory concepts to the topology of genome-scale metabolic networks. We identified three HCC subtypes with distinct differences in metabolic and signaling pathways and clinical survival and validated our results by performing additional experiments. We further identified HCC subtype-specific genes pivotal in controlling the entire metabolism and discovered genes that can be targeted for development of efficient treatment strategies for specific HCC subtypes. Our systems-level analyses provided a systematic way for characterization of HCC subtypes and identification of drug targets for effective treatment of HCC patients.
NETSeq reveals heterogeneous nucleotide incorporation by RNA polymerase I
Authors: Clarke Andrew M. , Engel Krysta L. , Giles Keith E. , Petit Chad M. , Schneider David A. 
Published: November 2018

SignificanceIt is well known that ribosomal RNA processing is directly impacted by the rate of transcription elongation by RNA polymerase I (Pol I). To understand how these processes are orchestrated, we must carefully define transcription elongation properties in vitro and in living cells. Here, we characterize DNA sequence elements that pause and terminate Pol I transcription in vitro. We also establish methods for analyzing Pol I transcription elongation properties in vivo using native elongating transcript sequencing (NETSeq). Our NETSeq data revealed frequent pausing by Pol I and decreased Pol I occupancy at G residues, suggesting unequal rates of nucleotide incorporation by the enzyme. These findings redefine our understanding of Pol I transcription elongation and its heterogeneity in vivo.
Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors
Authors: Peng Qin , Lu Shaoying , Shi Yuxin , Pan Yijia , Limsakul Praopim , Chernov Andrei V. , Qiu Juhui , Chai Xiaoqi , Shi Yiwen , Wang Pengzhi , Ji Yanmin , Li Yi-Shuan J. , Strongin Alex Y. , Verkhusha Vladislav V. , Izpisua Belmonte Juan Carlos , Ren Bing , Wang Yuanliang , Chien Shu , Wang Yingxiao 
Published: November 2018

Significance
We have developed a fluorescence resonance energy transfer (FRET) biosensor to visualize in single live cells the histone H3 Lys-9 trimethylation (H3K9me3) dynamics. Together with another FRET biosensor for simultaneous monitoring of the neighboring histone H3 Ser-10 phosphorylation (H3S10p) in the same cell, we found an anticorrelation between the dynamics of H3K9me3 and H3S10p during cell cycles, with H3S10p facilitating the decrease of H3K9me3 at onset of mitosis. This decrease of H3K9me3 is accompanied by dissolution of heterochromatin structures before chromatin condensation and nuclear envelope dissolution. The coordinated regulation of H3S10p and H3K9me3 may enhance access of remodeling complexes to the chromatin. Our results hence provide insights on how histone modifications and chromatin structures are coordinated to regulate mitosis.
Bottom–up modeling of chromatin segregation due to epigenetic modifications
Authors: MacPherson Quinn , Beltran Bruno , Spakowitz Andrew J. 
Published: November 2018

Significance
Predicting how epigenetic marks control the 3D organization of the genome is key to understanding how these marks regulate gene expression. We show that a physical model of a chromosome with experimentally measured local interactions segregates into euchromatin- and heterochromatin-like phases. The model reproduces many of the features of the large-scale organization of the chromosome as measured by Hi-C. Our work provides an estimate of the amount of epigenetic marking needed to segregate a gene into heterochromatin.
Benefits of phenotypic plasticity for population growth in varying environments
Authors: Xue BingKan , Leibler Stanislas 
Published: November 2018

Significance
Biological organisms show amazing abilities to change their forms and behavior according to their surroundings. For example, some caterpillars mimic flowers or twigs of the tree depending on their diet, freshwater snails grow thickened and deformed shells on sensing predator cues, and female aphids develop wings for migration if their habitat is crowded. Such flexibility in developing distinct external characteristics is known as “phenotypic plasticity,” often considered an adaptation strategy for surviving in variable environmental conditions. The prevalence of this phenomenon calls for a theoretical quantitative understanding of its evolutionary benefits. We use a simple model to illustrate how such benefits can be defined in terms of population growth rate and classify different contributions and limitations to those benefits.