bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Uncommon Initial Presentation of T-Cell/Histiocyte-Rich B-Cell Lymphoma
Authors: Filizoglu Nuh , Ones Tunc , Ozguven Salih , Turoglu Halil Turgut , Erdil Tanju Yusuf 
Published: December 2019

Abstract
T-cell/histiocyte-rich B-cell lymphoma accounts for approximately 1% to 3% of all cases of diffuse large B-cell lymphoma, and involvement of the kidneys comprises a mere 1% of the total primary extranodal lymphomas. We present a case of T-cell/histiocyte-rich B-cell lymphoma who had acute renal failure at initial presentation with bilateral lymphomatous infiltration depicted on FDG PET/CT scan. Four months after the treatment, a repeat FDG PET/CT scan revealed complete resolution of the renal lesions, indicative of the complete remission for kidneys.
The Relationship Between the Number of Ports and Surgical Outcomes in Laparoscopic Hepatectomy
Authors: Inoue Yoshihiro , Kitada Kazuya , Fujii Kensuke , Kagota Syuji , Tomioka Atsushi , Yamaguchi Toshifumi , Yokohama Keisuke , Ohama Hideko , Hamamoto Hiroki , Ishii Masatsugu , Osumi Wataru , Tsuchimoto Yusuke , Terazawa Tetsuji , Ogura Takeshi , Masubuchi Shinsuke , Yamamoto Masashi , Imoto Akira , Asai Akira , Komeda Koji , Fukunishi Shinya , Hirokawa Fumitoshi , Goto Masahiro , Tanaka Keitaro , Okuda Junji , Higuchi Kazuhide , Uchiyama Kazuhisa 
Published: December 2019

Introduction:
Reduced port surgery (RPS) has been garnering interest as a novel minimally invasive surgery lately.

Aim:
The authors examined the relationship between the number of ports and surgical outcomes after laparoscopic hepatectomy (LH).

Materials and Methods:
Between January 2012 and April 2019, 209 patients who underwent laparoscopic partial resection and lateral sectionectomy were retrospectively analyzed with respect to operative variables and surgical outcomes. Patients were divided into 5 groups by the number of ports used. Student’s t test, the χ2 test, the likelihood-ratio test, Fisher exact test, or Mann-Whitney U test were used to analyze the data.

Results:
Operative duration was significantly longer in patients with a larger number of ports than in those with a smaller number of ports. Chronological pain scores according to the visual analog scale (VAS) on postoperative days 1, 2, 4, and 7 were not associated with the number of ports and wound length in the umbilical region. The frequency of using additional analgesic agents was not significantly different between the groups. VAS scores and the number of additional analgesic agents used were smaller in patients in whom non–steroidal anti-inflammatory drugs were regularly administered postoperatively than in those in whom the drug was not regularly administered postoperatively. LH had a 3.4% complication rate (Clavien-Dindo classification >IIIA); however, this was not significantly different between the groups.

Conclusions:
No significant difference in postoperative pain was observed between RPS and conventional methods, although operative durations were shorter with RPS. However, RPS for LH may be associated with excellent cosmetic results compared with conventional methods.
Driving biology: The effect of standardized wound management on wound biomarker profiles
Authors: Dente Christopher John , Styrmisdottir Edda , Shi Audrey , Schobel Seth , Khatri Vivek , Potter Benjamin K. , Forsberg Jonathan A. , Buchman Timothy , Kirk Allan D. , Elster Eric 
Published: December 2019

BACKGROUND
The timing of coverage of an open wound is based on heavily on clinical gestalt. DoD's Surgical Critical Care Initiative created a clinical decision support tool that predicts wound closure success using clinical and biomarker data. The military uses a regimented protocol consisting of serial washouts and debridements. While decisions around wound closure in civilian centers are subject to the same clinical parameters, preclosure wound management is, generally, much more variable. We hypothesized that the variability in management would affect local biomarker expression within these patients.

METHODS
We compared data from 116 wounds in 73 military patients (MP) to similar data from 88 wounds in 78 civilian patients (CP). We used Wilcoxon rank-sum tests to assess concentrations of 32 individual biomarkers taken from wound effluent. Along with differences in the debridement frequency, we focused on these local biomarkers in MP and CP at both the first washout and the washout performed just prior to attempted closure.

RESULTS
On average, CP waited longer from the time of injury to closure (21.9 days, vs. 11.6 days, p < 0.0001) but had a similar number of washouts (3.86 vs. 3.44, p = 0.52). When comparing the wound effluent between the two populations, they had marked biochemical differences both when comparing the results at the first washout and at the time of closure. However, in a subset of civilian patients whose average number of days between washouts was never more than 72 hours, these differences ceased to be significant for most variables.

CONCLUSION
There were significant differences in the baseline biochemical makeup of wounds in the CP and MP. These differences could be eliminated if both were treated under similar wound care paradigms. Variations in therapy affect not only outcomes but also the actual biochemical makeup of wounds.

LEVEL OF EVIDENCE
Therapeutic, level IV.
A systematic review and meta-analysis evaluating geriatric consultation on older trauma patients
Authors: Eagles Debra , Godwin Bradley , Cheng Wei , Moors Joy , Figueira Sonshire , Khoury Lara , Fournier Karine , Lampron Jacinthe 
Published: December 2019

BACKGROUND
Early involvement of geriatrics is recommended for older trauma patients.

OBJECTIVE
This systematic review aimed to determine the impact of a geriatric assessment on mortality, hospital length of stay, discharge destination, and delirium incidence in patients 65 years and older admitted to a trauma center.

METHODS
The protocol was developed according to Preferred Reporting Items for Systematic Review and Meta-analysis guidelines and registered in PROSPERO (CRD42019131870). Search of five databases was completed April 2019. Two independent reviewers completed screening, full text review, and data abstraction. Meta-analysis was performed on outcomes with at least two studies.

RESULTS
A total of 928 unique citations were identified; eight were included in the final analysis. All were cohort studies, most of moderate to poor quality using the Newcastle-Ottawa Scale. We found hospital length of stay decreased by mean of 1.11 days (95% confidence interval, 0.79–1.43), but mortality was unchanged (odds ratio, 1.01; 95% confidence interval, 0.74–1.38) in older patients admitted to a trauma center who had a geriatric consultation. Meta-analysis of discharge destination and delirium incidence was not performed due to heterogeneity.

CONCLUSIONS
This is the first systematic review and meta-analysis to evaluate outcomes in older patients admitted to a trauma center after implementation of a geriatric trauma consultation service. We found a decrease in hospital length of stay but insufficient evidence of change in in-hospital mortality in older patients who received a geriatric consultation as part of their trauma care compared with those that received standard trauma care only. There is a need for more methodologically rigorous research in geriatric trauma.

LEVEL OF EVIDENCE
Systematic review and meta-analysis, level III.
Technical Considerations and Confounders for Urine CXCL10 Chemokine Measurement
Authors: Handschin Joelle , Hirt-Minkowski Patricia , Hönger Gideon , Mitrovic Sandra , Savic Prince Spasenija , Ho Julie , Nickerson Peter , Schaub Stefan 
Published: December 2019

Background.
The urine C-X-C motif chemokine 10 (CXCL10) is a promising screening biomarker for renal allograft rejection. The aim of the study was to investigate important technical and biological aspects as well as potential confounders when measuring urine CXCL10.

Methods.
We analyzed 595 urine samples from 117 patients, who participated in a randomized controlled trial investigating the clinical utility of urine CXCL10 monitoring for posttransplant management. Urine CXCL10 was measured by an immunoassay using electrochemiluminescence.

Results.
Intraassay coefficient of variation was 2.5%, and interassay coefficient of variation was 10%. Urine CXCL10 remained stable (ie, <10% degradation) for 8 hours at 25°C or 37°C and for 3 days at 4°C. CXCL10 concentrations [pg/mL] strongly correlated with urine CXCL10/creatinine ratios [ng/mmol] (r2 = 0.98; P < 0.0001). Leucocyturia and active BK-polyomavirus infection are associated with higher CXCL10 concentrations, while allograft function, serum CRP, patient age, proteinuria, urine pH, hematuria, squamous epithelia cell count, and bacteriuria did not correlate with urine CXCL10 concentrations. In 145 paired samples obtained within 1–2 weeks, 80% showed a CXCL10/creatinine ratio change of < ±2 ng/mmol or ±50%, respectively.

Conclusions.
Urine CXCL10 measurement on the used platform is accurate and robust. Leucocyturia and active BK-polyomavirus infection are major confounders, which can be easily detected but represent important diagnostic “blind spots” when using urine CXCL10 to screen for allograft rejection. The intraindividual biological variability of urine CXCL10 within 1–2 weeks is mostly below ±50%, which is still much higher than the technical variability due to sample handling/processing (<20%).
Simplified geometric representations of protein structures identify complementary interaction interfaces
Authors: McCafferty Caitlyn L. , Marcotte Edward M. , Taylor David W. 
Published: December 2019

ABSTRACTProtein-protein interactions are critical to protein function, but three-dimensional (3D) arrangements of interacting proteins have proven hard to predict, even given the identities and 3D structures of the interacting partners. Specifically, identifying the relevant pairwise interaction surfaces remains difficult, often relying on shape complementarity with molecular docking while accounting for molecular motions to optimize rigid 3D translations and rotations. However, such approaches can be computationally expensive, and faster, less accurate approximations may prove useful for large-scale prediction and assembly of 3D structures of multi-protein complexes. We asked if a reduced representation of protein geometry retains enough information about molecular properties to predict pairwise protein interaction interfaces that are tolerant of limited structural rearrangements. Here, we describe a cuboid transformation of 3D protein accessible surfaces on which molecular properties such as charge, hydrophobicity, and mutation rate can be easily mapped, implemented in the MorphProt package. Pairs of surfaces are compared to rapidly assess partner-specific potential surface complementarity. On two available benchmarks of 85 overall known protein complexes, we observed F1 scores (a weighted combination of precision and recall) of 19-34% at correctly identifying protein interaction surfaces, comparable to more computationally intensive 3D docking methods in the annual Critical Assessment of PRedicted Interactions. Furthermore, we examined the effect of molecular motion through normal mode simulation on a benchmark receptor-ligand pair and observed no marked loss of predictive accuracy for distortions of up to 6 Å RMSD. Thus, a cuboid transformation of protein surfaces retains considerable information about surface complementarity, offers enhanced speed of comparison relative to more complex geometric representations, and exhibits tolerance to conformational changes.
The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes
Authors: Sierra Maria A. , Bhattacharya Chandrima , Ryon Krista , Meierovich Sophie , Shaaban Heba , Westfall David , Mohammad Rawhi , Kuchin Katerina , Afshinnekoo Ebrahim , Danko David C. , Mason Christopher E. 
Published: December 2019

AbstractThe Microbe Directory (TMD) is a comprehensive database of annotations for microbial species collating features such as gram-stain, capsid-symmetry, resistance to antibiotics and more. This work presents a significant improvement to the original Microbe Directory (2018). This update adds 68,852 taxa, many new annotation features, an interface for the statistical analysis of microbiomes based on TMD features, and presents a portal for the broad community to add or correct entries. This update also adds curated lists of gene annotations which are useful for characterizing microbial genomes. Much of the new data in TMD is sourced from a set of databases and independent studies collating these data into a single quality controlled and curated source. This will allow researchers and clinicians to have easier access to microbial data and provide for the possibility of serendipitous discovery of otherwise unexpected trends.
Molecular Basis for the Evolved Instability of a Human G-Protein Coupled Receptor
Authors: Chamness Laura M. , Zelt Nathan B. , Kuntz Charles P. , Bender Brian J. , Penn Wesley D. , Ziarek Joshua J. , Meiler Jens , Schlebach Jonathan P. 
Published: December 2019

ABSTRACTMembrane proteins are prone to misfolding and degradation. This is particularly true for mammalian forms of the gonadotropin-releasing hormone receptor (GnRHR). Though they function at the plasma membrane, mammalian GnRHRs tend to accumulate within the secretory pathway. Their apparent instability is believed to have evolved in response to selection for attenuated GnRHR activity. Nevertheless, the structural basis of this adaptation remains unclear. We find that this adaptation coincides with a C-terminal truncation and an increase in the polarity of its transmembrane (TM) domains. This enhanced polarity compromises the translocon-mediated cotranslational folding of two TM domains. Moreover, replacing a conserved polar residue in TM6 with an ancestral hydrophobic residue partially restores GnRHR expression with minimal impact on function. An evolutionary analysis suggests variations in the polarity of this residue are associated with reproductive differences. Our findings suggest the marginal energetics of cotranslational folding can be exploited to tune membrane protein fitness.
CeutaOPEN: Individual-based field observations of breeding snowy ploversCharadrius nivosus
Authors: Eberhart-Phillips Luke J. , Cruz-López Medardo , Lozano-Angulo Lydia , del Ángel Salvador Gómez , Rojas-Abreu Wendoly , Küpper Clemens 
Published: December 2019

AbstractShorebirds (partimmembers of order Charadriiformes) have a global distribution and exhibit remarkable variation in ecological and behavioural traits that are pertinent to many core questions in the fields of evolutionary ecology and conservation biology. Shorebirds are also relatively convenient to study in the wild as they are ground nesting and often occupy open habitats that are tractable to monitor. Here we present a database documenting the reproductive ecology of 1,600 individually marked snowy plovers (Charadrius nivosus) monitored between 2006 and 2016 at Bahía de Ceuta (23°54 N, 106°57 W) – an important breeding site in north-western Mexico. The database encompasses various morphological, behavioural, and fitness-related traits of males and females along with spatial and temporal population dynamics. This open resource will serve as an important data repository for addressing overarching questions in avian ecology and wetland conservation during an era of big data and global collaborative science.
Characterization of the phototoxicity, chemigenetic profile, and mutational signatures of the chemotherapeutic CX-5461 inCaenorhabditis elegans
Authors: Ye Frank B. , Hamza Akil , Singh Tejomayee , Flibotte Stephane , Hieter Philip , O’Neil Nigel J. 
Published: December 2019

ABSTRACTNew anti-cancer therapeutics require extensivein vivocharacterization to identify endogenous and exogenous factors affecting efficacy, to measure toxicity and mutagenicity, and to determine genotypes resulting in therapeutic sensitivity or resistance. We usedCaenorhabditis elegansas a platform with which to characterize properties of anti-cancer therapeutic agentsin vivo. We generated a map of chemigenetic interactions between DNA damage response mutants and common DNA damaging agents. We used this map to investigate the properties of the new anti-cancer therapeutic CX-5461. We phenocopied the photoreactivity observed in CX-5461 clinical trials and found that CX-5461 generates reactive oxygen species when exposed to UVA radiation. We demonstrated that CX-5461 is a mutator, resulting in both large copy number variations and a high frequency of single nucleotide variations (SNVs). CX-5461-induced SNVs exhibited a distinct mutational signature. Consistent with the wide range of CX-5461-induced mutation types, we found that multiple repair pathways were needed for CX-5461 tolerance. Together, the data fromC. elegansdemonstrate that CX-5461 is a multimodal DNA damaging agent with strong similarity to ellipticines, a class of antineoplastic agents, and to anthracycline-based chemotherapeutics.
Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution
Authors: Sun Zhiyi , Vaisvila Romualdas , Yan Bo , Baum Chloe , Saleh Lana , Samaranayake Mala , Guan Shengxi , Dai Nan , Corrêa Ivan R. , Pradhan Sriharsa , Davis Theodore B. , Evans Thomas C. , Ettwiller Laurence M. 
Published: December 2019

AbstractThe predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisulfite treated DNA we applied a new enzymatic deamination approach, termed EM-seq (Enzymatic Methyl-seq) to long-range sequencing technologies. Our methodology, named LR-EM-seq (Long Range Enzymatic Methyl-seq) preserves the integrity of DNA allowing long-range methylation profiling of 5-mC and 5-hmC over several kilobases of genomic DNA. When applied to known differentially methylated regions (DMR), LR-EM-seq achieves phasing of over 5 kb resulting in broader and better defined DMRs compared to previously reported. This result demonstrated the importance of phasing methylation for biologically relevant questions and the applicability of LR-EM-seq for long range epigenetic analysis at single molecule and single nucleotide resolution.
The Nucleome Data Bank: Web-based Resources to Simulate and Analyze the Three-Dimensional Genome
Authors: Contessoto Vinícius G. , Cheng Ryan R. , Hajitaheri Arya , Dodero-Rojas Esteban , Mello Matheus F. , Lieberman-Aiden Erez , Wolynes Peter G. , Pierro Michele Di , Onuchic José N. 
Published: December 2019

AbstractWe introduce the Nucleome Data Bank, a web-based platform to simulate and analyze the three-dimensional organization of genomes. The Nucleome Data Bank enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and FISH data, as well as multiple observations of chromosomal dynamicsin vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the Nucleome Data Bank freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate three-dimensional structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The Nucleome Data Bank aims to be a shared resource to biologists, biophysicists, and all genome scientists. The Nucleome Data Bank (NDB) is available athttps://ndb.rice.edu.
New Tools for Genetically Targeting Myeloid Populations in the Central Nervous System
Authors: McKinsey Gabriel L. , Lizama Carlos O. , Keown-Lang Amber E. , Niu Abraham , Chee Elin , Santander Nicolas , Arnold Thomas D. 
Published: December 2019

AbstractAs the resident macrophages of the brain and spinal cord, microglia are crucial for the phagocytosis of infectious agents, apoptotic cells and synapses. Developmentally, microglia originate from the embryonic yolk sac and serve important roles in the sculpting of neonatal neural circuits. During brain injury or infection, bone-marrow derived macrophages invade neural tissue, making it difficult to distinguish between invading macrophages and resident microglia. In addition to circulation-derived monocytes, other non-microglial central nervous system (CNS) macrophage subtypes include borderzone (meningeal and perivascular) and choroid plexus macrophages. To distinguish between resident microglia and these other CNS macrophage subtypes, we generated aP2ry12-CreERmouse line. P2RY12 is a microglial-specific nucleotide sensing GPCR that is important for microglial response to tissue damage. Using immunofluorescent labeling and flow cytometry experiments, we show thatP2ry12-CreERrecombination is exceptionally specific to parenchymal microglia. We also perform ribosome immunoprecipitations and transcriptional profiling ofP2ry12-CreERrecombined cells, using a Cre-dependentRpl22-HAmouse line. By identifying genes enriched in this dataset that are not correspondingly enriched in a broaderCx3CR1-CreER; Rpl22dataset, we isolate a number of borderzone macrophage-specific transcripts, including the genePF4. Using aPF4-Cremouse line, we show thatPF4expression robustly marks borderzone macrophages. Together, we demonstrate two new methods to genetically target distinct CNS macrophage subtypes.
Dihydroartemisinin-loaded Magnetic Nanoparticles for Enhanced Chemodynamic Therapy
Authors: Guo Shengdi , Yao Xianxian , Jiang Qin , Wang Kuang , Zhang Yuanying , Peng Haibao , Tang Jing , Yang Wuli 
Published: December 2019

AbstractRecently, chemodynamic therapy (CDT) has represented a new approach for cancer treatment with low toxicity and side effects. Nonetheless, it has been a challenge to improve the therapeutic effect through increasing the amount of reactive oxygen species (ROS). Herein, we increased the amount of ROS agents in the Fenton-like reaction by loading dihydroartemisinin (DHA) which was an artemisinin (ART) derivative containing peroxide groups, into magnetic nanoparticles (MNP), thereby improving the therapeutic effect of CDT. Blank MNP were almost non-cytotoxic, whereas three MNP loading ART-based drugs, MNP-ART, MNP-DHA, and MNP-artesunate (MNP-AS), all showed significant killing effect on breast cancer cells (MCF-7 cells), in which MNP-DHA were the most potent. What’s more, the MNP-DHA showed high toxicity to drug-resistant breast cancer cells (MCF-7/ADR cells), demonstrating its ability to overcome multidrug resistance (MDR). The study revealed that MNP could produce ferrous ions under the acidic condition of tumor microenvironment, which catalyzed DHA to produce large amounts of ROS, leading to cell death. Further experiments also showed that the MNP-DHA had significant inhibitory effect on another two aggressive breast cancer cell lines (MDA-MB-231 and MDA-MB-453 cells), which indicated that the great potential of MNP-DHA for the treatment of intractable breast cancers.