bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth of the facultative chemolithoautotroph Ralstonia eutropha on organic waste materials: growth characteristics, redox regulation and hydrogenase activity
Authors: Poladyan Anna , Blbulyan Syuzanna , Sahakyan Mayramik , Lenz Oliver , Trchounian Armen 
Published: December 2019

AbstractBackgroundThe chemolithoautotrophic β-proteobacteriumRalstonia eutrophaH16 (Cupriavidus necator) is one of the most studied model organisms for growth on H2and CO2.R. eutrophaH16 is also a biologically significant bacterium capable of synthesizing O2-tolerant [NiFe]-hydrogenases (Hyds), which can be used as anode biocatalysts in enzyme fuel cells. For heterotrophic growth ofR. eutropha, various sources of organic carbon and energy can be used.ResultsGrowth, bioenergetic properties, and oxidation–reduction potential (ORP) kinetics were investigated during cultivation ofR. eutrophaH16 on fructose and glycerol or lignocellulose-containing brewery spent grain hydrolysate (BSGH). BSGH was used as carbon and energy source byR. eutrophaH16, and the activities of the membrane-bound hydrogenase (MBH) and cytoplasmic, soluble hydrogenase (SH) were measured in different growth phases. Growth ofR. eutrophaH16 on optimized BSGH medium yielded ~ 0.7 g cell dry weight L−1with 3.50 ± 0.02 (SH) and 2.3 ± 0.03 (MBH) U (mg protein)−1activities. Upon growth on fructose and glycerol, a pH drop from 7.0 to 6.7 and a concomitant decrease of ORP was observed. During growth on BSGH, in contrast, the pH and ORP stayed constant. The growth rate was slightly stimulated through addition of 1 mM K3[Fe(CN)6], whereas temporarily reduced growth was observed upon addition of 3 mM dithiothreitol. The overall andN,N′-dicyclohexylcarbodiimide-sensitive ATPase activities of membrane vesicles were ~ 4- and ~ 2.5-fold lower, respectively, upon growth on fructose and glycerol (FGN) compared with only fructose utilization (FN). Compared to FN, ORP was lower upon bacterial growth on FGN, GFN, and BSGH.ConclusionsOur results suggest that reductive conditions and low ATPase activity might be signals for energy depletion, which, in turn, leads to increased hydrogenase biosynthesis to overcome this unfavorable situation. Addition of fructose or microelements have no, or a negative, influence on hydrogenase activity. Organic wastes (glycerol, BSGH) are promising carbon and energy sources for the formation of biomass harboring significant amounts of the biotechnologically relevant hydrogenases MBH and SH. The results are valuable for using microbial cells as producers of hydrogenase enzymes as catalysts in enzymatic fuel cells.
Substantially improving the enantioconvergence of PvEH1, a Phaseolus vulgaris epoxide hydrolase, towards m-chlorostyrene oxide by laboratory evolution
Authors: Zong Xun-Cheng , Li Chuang , Xu Yao-Hui , Hu Die , Hu Bo-Chun , Zang Jia , Wu Min-Chen 
Published: December 2019

Abstract
Background
Epoxide hydrolase can regioselectively catalyze the oxirane ring-opening hydrolysis of rac-epoxides producing the corresponding chiral diols. In our laboratory, a gene named pveh1 encoding an EH from Phaseolus vulgaris was cloned. Although the directed modification of PvEH1 was carried out, the mutant PvEH1Y3 showed a limited degree of enantioconvergence towards racemic (rac-) m-chlorostyrene oxide (mCSO).

Results
PvEH1 and PvEH1Y3 were combinatively subjected to laboratory evolution to further enhance the enantioconvergence of PvEH1Y3 towards rac-mCSO. Firstly, the substrate-binding pocket of PvEH1 was identified using a CAVER 3.0 software, and divided into three zones. After all residues in zones 1 and 3 were subjected to leucine scanning, two E. coli transformants, E. coli/pveh1Y149L and /pveh1P184L, were selected, by which rac-mCSO was transformed into (R)-m-chlorophenyl-1,2-ethanediol (mCPED) having 55.1% and 27.2% eep. Secondly, two saturation mutagenesis libraries, E. coli/pveh1Y149X and /pveh1P184X (X: any one of 20 residues) were created at sites Y149 and P184 of PvEH1. Among all transformants, both E. coli/pveh1Y149L (65.8% αS and 55.1% eep) and /pveh1P184W (66.6% αS and 59.8% eep) possessed the highest enantioconvergences. Finally, the combinatorial mutagenesis was conducted by replacements of both Y149L and P184W in PvEH1Y3, constructing E. coli/pveh1Y3Z2, whose αS reached 97.5%, higher than that (75.3%) of E. coli/pveh1Y3. In addition, the enantioconvergent hydrolysis of 20 mM rac-mCSO was performed by E. coli/pveh1Y3Z2, giving (R)-mCPED with 95.2% eep and 97.2% yield.

Conclusions
In summary, the enantioconvergence of PvEH1Y3Z2 was successfully improved by laboratory evolution, which was based on the study of substrate-binding pocket by leucine scanning. Our present work introduced an effective strategy for the directed modification of enantioconvergence of PvEH1.
Optimization of an in vivo model to study immunity to Plasmodium falciparum pre-erythrocytic stages
Authors: Flores-Garcia Yevel , Herrera Sonia M. , Jhun Hugo , Pérez-Ramos Daniel W. , King C. Richter , Locke Emily , Raghunandan Ramadevi , Zavala Fidel 
Published: December 2019

Abstract
Background
The circumsporozoite protein (CSP) of Plasmodium is a key surface antigen that induces antibodies and T-cells, conferring immune protection in animal models and humans. However, much of the work on CSP and immunity has been developed based on studies using rodent or non-human primate CSP antigens, which may not be entirely translatable to CSP expressed by human malaria parasites, especially considering the host specificity of the different species.

Methods
Using a genetically engineered strain of Plasmodium berghei that expresses luciferase, GFP and the Plasmodium falciparum orthologue of CSP, the effect of laboratory preparation, mosquito treatment and mouse factors on sporozoite infectivity was assessed using an in vivo bioluminescence assay on mice. This assay was compared with a PCR-based protection assay using an already described monoclonal antibody that can provide sterile protection against sporozoite challenge.

Results
Bioluminescence assay demonstrated similar detection levels of the quantity and kinetics of liver-stage infection, compared to PCR-based detection. This assay was used to evaluate treatment of sporozoite and delivery method on mouse infectivity, as well as the effects of age, sex and strain of mice. Finally, this assay was used to test the protective capacity of monoclonal antibody AB317; results strongly recapitulate the findings of previous work on this antibody.

Conclusions
The PbGFP-Luc line and in vivo bioluminescence imaging provide highly sensitive read-outs of liver-stage infection in mice, and this method can be useful to reliably evaluate potency of pre-erythrocytic interventions.
Intracluster correlation coefficients in the Greater Mekong Subregion for sample size calculations of cluster randomized malaria trials
Authors: Peerawaranun Pimnara , Landier Jordi , Nosten Francois H. , Nguyen Thuy-Nhien , Hien Tran Tinh , Tripura Rupam , Peto Thomas J. , Phommasone Koukeo , Mayxay Mayfong , Day Nicholas P. J. , Dondorp Arjen , White Nick , von Seidlein Lorenz , Mukaka Mavuto 
Published: December 2019

AbstractBackgroundSample size calculations for cluster randomized trials are a recognized methodological challenge for malaria research in pre-elimination settings. Positively correlated responses from the participants in the same cluster are a key feature in the estimated sample size required for a cluster randomized trial. The degree of correlation is measured by the intracluster correlation coefficient (ICC) where a higher coefficient suggests a closer correlation hence less heterogeneity within clusters but more heterogeneity between clusters.MethodsData on uPCR-detectedPlasmodium falciparumandPlasmodium vivaxinfections from a recent cluster randomized trial which aimed at interrupting malaria transmission through mass drug administrations were used to calculate the ICCs for prevalence and incidence ofPlasmodiuminfections. The trial was conducted in four countries in the Greater Mekong Subregion, Laos, Myanmar, Vietnam and Cambodia. Exact and simulation approaches were used to estimate ICC values for both the prevalence and the incidence of parasitaemia. In addition, the latent variable approach to estimate ICCs for the prevalence was utilized.ResultsThe ICCs for prevalence ranged between 0.001 and 0.082 for all countries. The ICC from the combined 16 villages in the Greater Mekong Subregion were 0.26 and 0.21 forP.falciparumandP. vivaxrespectively. The ICCs for incidence of parasitaemia ranged between 0.002 and 0.075 for Myanmar, Cambodia and Vietnam. There were very high ICCs for incidence in the range of 0.701 to 0.806 in Laos during follow-up.ConclusionICC estimates can help researchers when designing malaria cluster randomized trials. A high variability in ICCs and hence sample size requirements between study sites was observed. Realistic sample size estimates for cluster randomized malaria trials in the Greater Mekong Subregion have to assume high between cluster heterogeneity and ICCs. This work focused on uPCR-detected infections; there remains a need to develop more ICC references for trials designed around prevalence and incidence of clinical outcomes. Adequately powered trials are critical to estimate the benefit of interventions to malaria in a reliable and reproducible fashion.Trial registration: ClinicalTrials.govNCT01872702. Registered 7 June 2013. Retrospectively registered.https://clinicaltrials.gov/ct2/show/NCT01872702
Intrafractional 6D head movement increases with time of mask fixation during stereotactic intracranial RT-sessions
Authors: Mangesius Julian , Seppi Thomas , Weigel Rocco , Arnold Christoph Reinhold , Vasiljevic Danijela , Goebel Georg , Lukas Peter , Ganswindt Ute , Nevinny-Stickel Meinhard 
Published: December 2019

Abstract
Background
The present study investigates the intrafractional accuracy of a frameless thermoplastic mask used for head immobilization during stereotactic radiotherapy. Non-invasive masks cannot completely prohibit head movements. Previous studies attempted to estimate the magnitude of intrafractional inaccuracy by means of pre- and postfractional measurements only. However, this might not be sufficient to accurately map also intrafractional head movements.

Materials and methods
Intrafractional deviation of mask-fixed head positions was measured in five patients during a total of 94 fractions by means of close-meshed repeated ExacTrac measurements (every 1.4 min) conducted during the entire treatment session. A median of six (range: 4 to 11) measurements were recorded per fraction, delivering a dataset of 453 measurements.

Results
Random errors (SD) for the x, y and z axes were 0.27 mm, 0.29 mm and 0.29 mm, respectively. Median 3D deviation was 0.29 mm. Of all 3D intrafractional motions, 5.5 and 0.4% exceeded 1 mm and 2 mm, respectively. A moderate correlation between treatment duration and mean 3D displacement was determined (rs = 0.45). Mean 3D deviation increased from 0.21 mm (SD = 0.26 mm) in the first 2 min to a maximum of 0.53 mm (SD = 0.31 mm) after 10 min of treatment time.

Conclusion
Pre- and post-treatment measurement is not sufficient to adequately determine the range of intrafractional head motion. Thermoplastic masks provide both reliable interfractional and intrafractional immobilization for image-guided stereotactic hypofractionated radiotherapy. Greater positioning accuracy may be obtained by reducing treatment duration (< 6 min) and applying intrafractional correction.

Trial registration
Clinicaltrials.gov, NCT03896555, Registered 01 April 2019 - retrospectively registered.
Intramedullary nailing for pertrochanteric fractures of proximal femur: a consecutive series of 323 patients treated with two devices
Authors: Catania Pompeo , Passaretti Daniele , Montemurro Giorgio , Ripanti Simone , Carbone Stefano , Candela Vittorio , Carnovale Michele , Gumina Stefano , Pallotta Francecsco 
Published: December 2019

Abstract
Introduction
Pertrochanteric fractures (PFs) frequently affect the lower limb of osteoporotic patients and represent an important cause of morbidity and mortality in the elderly. In this prospective randomized controlled trial, we have compared functional and radiological results and complications of patients affected by PFs treated with two intramedullary proximal femoral nails.

Materials
We enrolled 323 subjects with PFs, classified according to AO/OTA system as 31.A1 (pertrochanteric simple) and 31.A2 (pertrochanteric multifragmentary). Patients were divided into two groups according to the osteosynthesis devices: group A, Elos-Intrauma® nail (155 cases) and group B, Gamma 3-Stryker® nail (168 cases). Pre-operatively, the baseline characteristics of each patient (gender, age, weight and BMI) were collected. Intraoperative blood loss, subjective pain by visual analogue scale (VAS), esthetic satisfaction, functional scores of the hip by Harris Hip Score (HHS), and Western Ontario and McMaster Universities Arthritis Index (WOMAC) were noted. The post-operative degree of fracture reduction was assessed. Each patient had a minimum follow-up of 12 months.

Results
The study group was composed of 106 male and 217 female with an average age of 85.4 (range, 65–90, standard deviation (SD) 5.95) years. No statistical differences about sex and age distribution were noted between the two groups. Group A reported lower intraoperative blood loss, 45 ml vs 51 ml, respectively (p < 0.001). There was not any statistical difference about operative time. Group A had a better reduction of fracture (p = 0.0347). The greatest difference was detectable comparing subgroups 31.A2 (p = 0.032). There were no statistical differences about complication frequency and the overall rate was 25% (80 cases). Finally, there was no difference in terms of VAS, HHS, and WOMAC score between the two groups on each follow-up. Patients of group A showed a higher subjective satisfaction index at 1 post-operative year, 7.42 (SD 1.19) vs 6.45 (SD 1.35) of group B (p < 0.001).

Conclusion
Elos® nail is a reliable device on a short-term follow-up and represents an alternative choice to the Gamma 3® nail, a well-known and appreciated system for over 25 years.
Biofilm production of coagulase-negative staphylococci isolated from rescued wild animals in the Republic of Korea
Authors: Lee Sangjun , Hwang Jehwi , Kim Jongwoon , Lee Joonyeop , Kim Hong-Cheul , Rhim Haerin , Han Jae-Ik 
Published: December 2019

Abstract
Biofilm production is a well-known causative factor of catheter- and medical device-related sepsis. Its high prevalence in coagulase-negative staphylococci (CoNS) has recently been reported. Information on biofilm production in CoNS isolated from wild animals is lacking. Herein, we studied the biofilm formation capabilities of CoNS isolated from rescued wild animals in the Republic of Korea. Swab samples were collected from the conjunctiva, nasal cavity, perianal area, and rectum for mammals while the sampling was done from the conjunctiva, oral mucosa, pericloacal area, and cloaca for birds. Isolation of CoNS was based on morphological and biochemical analyses along with molecular typing. Biofilm production was analyzed using 96-well plate based quantitative adherence assays. The studies demonstrated that CoNS of mammalian origin have higher biofilm-producing ability (70.4%) than the isolates from birds (62.5%). In particular, all methicillin-resistant (MR) CoNS isolated from mammals were capable of biofilm formation while only 63.3% of MR CoNS isolated from birds could produce biofilms. The MR CoNS isolated from mammals also had a significantly higher ability to form biofilms (100%) than methicillin susceptible CoNS (60.0%) than those isolates from birds. The findings show that wild animals may act as reservoirs as well as possible transmitters of biofilm-mediated antibiotic resistant genes.
Up-regulation of IGF2BP2 by multiple mechanisms in pancreatic cancer promotes cancer proliferation by activating the PI3K/Akt signaling pathway
Authors: Xu Xiaodong , Yu Yan , Zong Ke , Lv Pengwei , Gu Yuantin 
Published: December 2019

Abstract
Background
The survival of pancreatic cancer patients remains poor. However, the underlying molecular mechanism and new therapeutic target of pancreatic cancer are still needed to be found. Many studies have shown that the IGF2 mRNA-binding protein 2 (IGF2BP2) plays oncogenic roles in cancers. However, the clinical significance, role and molecular mechanisms of IGF2BP2 in pancreatic cancer remain unclear.

Methods
The expression of IGF2BP2 and miR-141 was detected in pancreatic cancer, and clinical significances were analyzed by statistical analysis. The function of IGF2BP2 and miR-141 was determined in vitro and in vivo, and the underlying mechanism was investigated. The gene copy number variation (CNV) of IGF2BP2 was analyzed based on The Cancer Genome Atlas (TCGA) dataset. microRNAs (miRNAs) regulating IGF2BP2 were predicted by online tools and confirmed by experiments.

Results
IGF2BP2 is overexpressed in pancreatic cancer tissues compared with control tissues. Upregulation of IGF2BP2 predicts shorter overall survival (OS) in pancreatic cancer patients by statistical analysis. IGF2BP2 overexpression is partially due to genomic amplification. Bioinformatics analyses and validation experiments showed that IGF2BP2 is a direct target of miR-141. A negative correlation between IGF2BP2 mRNA expression and the expression of miR-141 was observed in pancreatic cancer tissues and more importantly, reexpression of miR-141 rescued the oncogenic role of IGF2BP2. Moreover, upregulating IGF2BP2 expression promotes pancreatic cancer cell growth by activating the PI3K/Akt signaling pathway in vitro and in vivo.

Conclusions
We comprehensively reveal the oncogenic role of IGF2BP2 in pancreatic cancer carcinogenesis and confirm that genomic amplification and the silencing of miR-141 contribute to its activation. Our findings highlight that IGF2BP2 may be a promising molecular target for the treatment of pancreatic cancer.
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
Authors: An Lin , Yang Tao , Yang Jiahao , Nuebler Johannes , Xiang Guanjue , Hardison Ross C. , Li Qunhua , Zhang Yu 
Published: December 2019

AbstractThe spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically associating domains (TADs), within which most of the regulatory interactions are thought to occur. TADs are not homogeneous structural units but appear to be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, to identify hierarchical TADs. OnTAD reveals new biological insights into the role of different TAD levels, boundary usage in gene regulation, the loop extrusion model, and compartmental domains. OnTAD is available at https://github.com/anlin00007/OnTAD.
Right Dose Right Now: bedside data-driven personalized antibiotic dosing in severe sepsis and septic shock — rationale and design of a multicenter randomized controlled superiority trial
Authors: Roggeveen Luca F. , Fleuren Lucas M. , Guo Tingjie , Thoral Patrick , de Grooth Harm Jan , Swart Eleonora L. , Klausch Thomas L. T. , van der Voort Peter H. J. , Girbes Armand R. J. , Bosman Rob J. , Elbers Paul W. G. 
Published: December 2019

Abstract
Background
Antibiotic exposure is often inadequate in critically ill patients with severe sepsis or septic shock and this is associated with worse outcomes. Despite markedly altered and rapidly changing pharmacokinetics in these patients, guidelines and clinicians continue to rely on standard dosing schemes. To address this challenge, we developed AutoKinetics, a clinical decision support system for antibiotic dosing. By feeding large amounts of electronic health record patient data into pharmacokinetic models, patient-specific predicted future plasma concentrations are displayed graphically. In addition, a tailored dosing advice is provided at the bedside in real time. To evaluate the effect of AutoKinetics on pharmacometric and clinical endpoints, we are conducting the Right Dose Right Now multicenter, randomized controlled, two-arm, parallel-group, non-blinded, superiority trial.

Methods
All adult intensive care patients with a suspected or proven infection and having either lactatemia or receiving vasopressor support are eligible for inclusion. Randomization to the AutoKinetics or control group is initiated at the bedside when prescribing at least one of four commonly administered antibiotics: ceftriaxone, ciprofloxacin, meropenem and vancomycin. Dosing advice is available for patients in the AutoKinetics group, whereas patients in the control group receive standard dosing.
The primary outcome of the study is pharmacometric target attainment during the first 24 h. Power analysis revealed the need for inclusion of 42 patients per group per antibiotic. Thus, a total of 336 patients will be included, 168 in each group. Secondary pharmacometric endpoints include time to target attainment and fraction of target attainment during an entire antibiotic course. Secondary clinical endpoints include mortality, clinical cure and days free from organ support. Several other exploratory and subgroup analyses are planned.

Discussion
This is the first randomized controlled trial to assess the effectiveness and safety of bedside data-driven automated antibiotic dosing advice. This is important as adequate antibiotic exposure may be crucial to treat severe sepsis and septic shock. In addition, the trial could prove to be a significant contribution to clinical pharmacometrics and serve as a stepping stone for the use of big data and artificial intelligence in the field.

Trial registration
Netherlands Trial Register (NTR), NL6501/NTR6689. Registered on 25 August 2017.
European Clinical Trials Database (EudraCT), 2017-002478-37. Registered on 6 November 2017.