bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes of Robotic Living Donor Right Hepatectomy From 52 Consecutive Cases
Authors: Rho Seoung Yoon , Lee Jae Geun , Joo Dong Jin , Kim Myoung Soo , Kim Soon Il , Han Dai Hoon , Choi Jin Sub , Choi Gi Hong 
Published: August 2020

Objective:
To investigate the feasibility and safety of RLDRH

Summary of Background Data:
Data for minimally invasive living-donor right hepatectomy, especially RLDRH, from a relatively large donor cohort that have not been reported yet.

Methods:
From March 2016 to March 2019, 52 liver donors underwent RLDRH. The clinical and perioperative outcomes of RLDRH were compared with those of CODRH (n = 62) and LADRH (n = 118). Donor satisfaction with cosmetic results was compared between RLDRH and LADRH using a body image questionnaire.

Results:
Although RLDRH was associated with longer operative time (minutes) (RLDRH, 493.6; CODRH, 404.4; LADRH, 355.9; P < 0.001), mean estimated blood loss (mL) was significantly lower (RLDRH, 109.8; CODRH, 287.1; LADRH, 265.5; P = 0.001). Postoperative complication rates were similar among the 3 groups (RLDRH, 23.1%; CODRH, 35.5%; LADRH, 28.0%; P = 0.420). Regarding donor satisfaction, body image and cosmetic appearance scores were significantly higher in RLDRH than in LADRH. After propensity score matching, RLDRH showed less estimated blood loss compared to those of CODRH (RLDRH, 114.7 mL; CODRH, 318.4 mL; P < 0.001), but complication rates were similar among the three groups (P = 0.748).

Conclusions:
RLDRH resulted in less blood loss compared with that of CODRH and similar postoperative complication rates to CODRH and LADRH. RLDRH provided better body image and cosmetic results compared with those of LADRH. RLDRH is feasible and safe when performed by surgeons experienced with both robotic and open hepatectomy.
Plasma resuscitation with adjunctive peritoneal resuscitation reduces ischemic intestinal injury following hemorrhagic shock
Authors: Schucht Jessica E. , Matheson Paul J. , Harbrecht Brian G. , Bond Logan , Jones Shawn , Alkhateeb Khaled J. M. , Ashkettle Graham R. , Smith Jason W. 
Published: August 2020

INTRODUCTION
Impaired intestinal microvascular perfusion following resuscitated hemorrhagic shock (HS) leads to ischemia-reperfusion injury, microvascular dysfunction, and intestinal epithelial injury, which contribute to the development of multiple organ dysfunction syndrome in some trauma patients. Restoration of central hemodynamics with traditional methods alone often fails to fully restore microvascular perfusion and does not protect against ischemia-reperfusion injury. We hypothesized that resuscitation (RES) with fresh frozen plasma (FFP) alone or combined with direct peritoneal resuscitation (DPR) with 2.5% Delflex solution might improve blood flow and decrease intestinal injury compared with conventional RES or RES with DPR alone.

METHODS
Sprague-Dawley rats underwent HS (40% mean arterial pressure) for 60 minutes and were randomly assigned to a RES group (n = 8): sham, HS–crystalloid resuscitation (CR) (shed blood + two volumes CR), HS-CR-DPR (intraperitoneal 2.5% peritoneal dialysis fluid), HS-FFP (shed blood + two volumes FFP), and HS-DPR-FFP (intraperitoneal dialysis fluid + two volumes FFP). Laser Doppler flowmeter evaluation of the ileum, serum samples for fatty acid binding protein enzyme-linked immunosorbent assay, and hematoxylin and eosin (H&E) staining were used to assess intestinal injury and blood flow. p Values of <0.05 were considered significant.

RESULTS
Following HS, the addition of DPR to either RES modality improved intestinal blood flow. Four hours after resuscitated HS, FABP-2 (intestinal) and FABP-6 (ileal) were elevated in the CR group but reduced in the FFP and DPR groups. The H&E staining demonstrated disrupted intestinal villi in the FFP and CR groups, most significantly in the CR group. Combination therapy with FFP and DPR demonstrated negligible cellular injury in H&E graded samples and a significant reduction in fatty acid binding protein levels.

CONCLUSION
Hemorrhagic shock leads to ischemic-reperfusion injury of the intestine, and both FFP and DPR alone attenuated intestinal damage; combination FFP-DPR therapy alleviated most signs of organ injury. Resuscitation with FFP-DPR to restore intestinal blood flow following shock could be an essential method of reducing morbidity and mortality after trauma.
Stop flailing: The impact of bicortically displaced rib fractures on pulmonary outcomes in patients with chest trauma — an American Association for the Surgery of Trauma multi-institutional study
Authors: Senekjian Lara , Birkas Yekaterina , Buhavac Milos , Dayal Saraswati , Mukherjee Kaushik , Nygaard Rachel , Pierce Sean , Buaza Graciella , Sperry Jason , Eriksson Evert , Leon Stuart M. , Kopelman Tammy , Spadafore Philomene , Kopatsis Anthony , Moore Forrest , Taylor Annette , Colonna Alexander , Enniss Toby , McCrum Marta , Nunez Jade , Young Jason , Nirula Raminder 
Published: August 2020

BACKGROUND
Current evaluation of rib fractures focuses almost exclusively on flail chest with little attention on bicortically displaced fractures. Chest trauma that is severe enough to cause fractures leads to worse outcomes. An association between bicortically displaced rib fractures and pulmonary outcomes would potentially change patient care in the setting of trauma. We tested the hypothesis that bicortically displaced fractures were an important clinical marker for pulmonary outcomes in patients with nonflail rib fractures.

METHODS
This nine-center American Association for the Surgery of Trauma multi-institutional study analyzed adults with two or more rib fractures. Admission computerized tomography scans were independently reviewed. The location, degree of rib fractures, and pulmonary contusions were categorized. Univariate and multivariate logistic regression analyses were performed to identify independent predictors of pneumonia, acute respiratory distress syndrome (ARDS), and tracheostomy. Analyses were performed in nonflail patients and also while controlling for flail chest to determine if bicortically displaced fractures were independently associated with outcomes.

RESULTS
Of the 1,110 patients, 103 (9.3%) developed pneumonia, 78 (7.0%) required tracheostomy, and 30 (2.7%) developed ARDS. Bicortically displaced fractures were present in 277 (25%) of patients and in 206 (20.3%) of patients without flail chest. After adjusting for patient demographics, injury, and admission physiology, negative pulmonary outcomes occurred over twice as frequently in those with bicortically displaced fractures without flail chest (n = 206) when compared with those without bicortically displaced fractures—pneumonia (odds ratio [OR], 2.0; 95% confidence interval [CI], 1.1–3.6), ARDS (OR, 2.6; 95% CI, 1.0–6.8), and tracheostomy (OR, 2.7; 95% CI, 1.4–5.2). When adjusting for the presence of flail chest, bicortically displaced fractures remained an independent predictor of pneumonia, tracheostomy, and ARDS.

CONCLUSION
Patients with bicortically displaced rib fractures are more likely to develop pneumonia, ARDS, and need for tracheostomy even when controlling for flail chest. Future studies should investigate the utility of flail chest management algorithms in patients with bicortically displaced fractures.

LEVEL OF EVIDENCE
Prognostic and epidemiological study, level III.
A Detailed View of KIR Haplotype Structures and Gene Families as Provided by a New Motif-based Multiple Sequence Alignment
Authors: Roe David , Vierra-Green Cynthia , Pyo Chul-Woo , Geraghty Daniel E. , Spellman Stephen R. , Maiers Martin , Kuang Rui 
Published: August 2020

AbstractHuman chromosome 19q13.4 contains genes encoding killer-cell immunoglobulin-like receptors (KIR). Reported haplotype lengths range from 67 to 269 kilobases and contain 4 to 18 genes. The region has certain properties such as single nucleotide variation, structural variation, homology, and repetitive elements that make it hard to align accurately beyond single gene alleles. To the best of our knowledge, a multiple sequence alignment of KIR haplotypes has never been published or presented. Such an alignment would be useful to precisely define KIR haplotypes and loci, provide context for assigning alleles (especially fusion alleles) to genes, infer evolutionary history, impute alleles, interpret and predict co-expression, and generate markers. In order to extend the framework of KIR haplotype sequences in the human genome reference, 27 new sequences were generated including 24 haplotypes from 12 individuals of African American ancestry that were selected for genotypic diversity and novelty to the reference, to bring the total to 68 full length genomic KIR haplotype sequences. We leveraged these data and tools from our long-read KIR haplotype assembly algorithm to define and align KIR haplotypes at <5 kb resolution on average. We then used a standard alignment algorithm to refine that alignment down to single base resolution. This processing demonstrated that the high-level alignment recapitulates human-curated annotation of the human haplotypes as well as a chimpanzee haplotype. Further, assignments and alignments of gene alleles were consistent with their human curation in haplotype and allele databases. These results define KIR haplotypes as 14 loci containing 9 genes. The multiple sequence alignments have been applied in two software packages as probes to capture and annotate KIR haplotypes and as markers to genotype KIR from WGS.
Ig-VAE: Generative Modeling of Protein Structure by Direct 3D Coordinate Generation
Authors: Eguchi Raphael R. , Choe Christian A. , Huang Po-Ssu 
Published: August 2020

AbstractWhile deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.
The inner membrane protein YhdP modulates the rate of anterograde phospholipid flow inEscherichia coli
Authors: Grimm Jacqueline , Shi Handuo , Wang Wei , Mitchell Angela M. , Wingreen Ned S. , Huang Kerwyn Casey , Silhavy Thomas J. 
Published: August 2020

AbstractThe outer membrane (OM) of Gram-negative bacteria is a selective permeability barrier that allows uptake of nutrients while simultaneously protecting the cell from harmful compounds. The basic pathways and molecular machinery responsible for transporting lipopolysaccharides (LPS), lipoproteins, and β-barrel proteins to the OM have been identified, but very little is known about phospholipid (PL) transport. To identify genes capable of affecting PL transport, we screened for genetic interactions withmlaA*, a mutant in which anterograde PL transport causes the inner membrane (IM) to shrink and eventually rupture; characterization ofmlaA*-mediated lysis suggested that PL transport can occur via a high-flux, diffusive flow mechanism. We found that YhdP, an IM protein involved in maintaining the OM permeability barrier, modulates the rate of PL transport duringmlaA*-mediated lysis. Deletion ofyhdPfrommlaA* reduced the rate of IM transport to the OM by 50%, slowing shrinkage of the IM and delaying lysis. As a result, the weakened OM of ΔydhPcells was further compromised and ruptured before the IM duringmlaA*-mediated death. These findings demonstrate the existence of a high-flux, diffusive pathway for PL flow inEscherichia colithat is modulated by YhdP.Significance StatementThe outer membrane (OM) of Gram-negative bacteria serves as a barrier that protects cells from harmful chemical compounds, including many antibiotics. Understanding how bacteria build this barrier is an important step in engineering strategies to circumvent it. A long-standing mystery in the field is how phospholipids (PLs) are transported from the inner membrane (IM) to the OM. We previously discovered that a mutation in the genemlaAcauses rapid flow of PLs to the OM, eventually resulting in IM rupture. Here, we found that deletion of the geneyhdPdelayed cell death in themlaAmutant by slowing flow of PLs to the OM. These findings reveal a high-flux, diffusive pathway for PL transport in Gram-negative bacteria modulated by YhdP.
Evaluation of Alginate-Based Bioinks for 3D Bioprinting, Mesenchymal Stromal Cell Osteogenesis, and Application for Patient-Specific Bone Grafts
Authors: Gonzalez-Fernandez Tomas , Tenorio Alejandro J. , Campbell Kevin T. , Silva Eduardo A. , Leach J. Kent 
Published: August 2020

AbstractTo realize the promise of 3D bioprinting, it is imperative to develop bioinks that possess the biological and rheological characteristics needed for the printing of cell-laden tissue grafts. Alginate is widely used as a bioink because its rheological properties can be modified through pre-crosslinking or the addition of thickening agents to increase printing resolution. However, modification of alginate’s physicochemical characteristics using common crosslinking agents can affect its cytocompatibility. Therefore, we evaluated the printability, physicochemical properties, and osteogenic potential of four common alginate bioinks: alginate-CaCl2(alg-CaCl2), alginate-CaSO4(alg-CaSO4), alginate-gelatin (alg-gel) and alginate-nanocellulose (alg-ncel) for the 3D bioprinting of patient-specific osteogenic grafts. While all bioinks possessed similar viscosity, printing fidelity was lower in the pre-crosslinked bioinks. When used to print geometrically defined constructs, alg-CaSO4and alg-ncel exhibited higher mechanical properties and lower mesh size than those printed with alg-CaCl2or alg-gel. The physical properties of these constructs affected the biological performance of encapsulated bone marrow-derived mesenchymal stromal cells (MSCs). Cell-laden constructs printed using alg-CaSO4and alg-ncel exhibited greater cell apoptosis and contained fewer living cells 7 days post-printing. In addition, effective cell-matrix interactions were only observed in alg-CaCl2printed constructs. When cultured in osteogenic media, MSCs in alg-CaCl2constructs exhibited increased osteogenic differentiation compared to the other three bioinks. This bioink was then used to 3D print anatomically accurate cell-laden scaphoid bones that were capable of partial mineralization after 14 days ofin vitroculture. These results highlight the importance of bioink properties to modulate cell behavior and the biofabrication of clinically relevant bone tissues.
An AI-powered blood test to detect cancer using nanoDSF
Authors: Tsvetkov Philipp O. , Eyraud Rémi , Ayache Stéphane , Bougaev Anton A. , Malesinski Soazig , Benazha Hamed , Gorokhova Svetlana , Buffat Christophe , Dehais Caroline , Sanson Marc , Bielle Franck , Figarella-Branger Dominique , Chinot Olivier , Tabouret Emeline , Devred François 
Published: August 2020

AbstractWe describe a novel cancer diagnostic method based on plasma denaturation profiles obtained by a non-conventional use of Differential Scanning Fluorimetry. We show that 84 glioma patients and 63 healthy controls can be automatically classified using denaturation profiles with the help of machine learning algorithms with 92% accuracy. Proposed high throughput workflow can be applied to any type of cancer and could become a powerful pan-cancer diagnostic and monitoring tool from a simple blood test.
P2X receptors inAplysia californica: Chemosensory systems, bio-energetic and development
Authors: Györi János , Kohn Andrea B. , Moroz Leonid L. 
Published: August 2020

AbstractATP and its ionotropic P2X receptors are components of one of the most ancient signaling systems. However, little is known about the distribution and function of purinergic transmission in invertebrates. Here, we cloned, expressed, and pharmacologically characterized P2X receptors in the sea slugAplysia californica– a prominent model in cellular and system neuroscience. We showed that ATP and P2X receptors are essential signaling components within the unique bioenergetic center located in the CNS ofAplysia, also known as the cerebral F-cluster of insulin-containing neurons. Functional P2X receptors were successfully expressed inXenopusoocytes to characterize their ATP-dependence (EC50=306μM), two-phased kinetics, ion selectivity (Na+-dependence), sensitivity to the ATP analog Bz-ATP (~20% compare to ATP) and antagonists (with PPADS as a more potent inhibitor compared to suramin). Next, using RNA-seq, we characterized the expression of P2X receptors across more than a dozenAplysiaperipheral tissues and developmental stages. We showed that P2X receptors are predominantly expressed in chemosensory structures and during early cleavage stages. The localization and pharmacology of P2X receptors inAplysiahighlight the evolutionary conservation of bioenergetic sensors and chemosensory purinergic transmission across animals. This study also provides a foundation to decipher homeostatic mechanisms in development and neuroendocrine systems.Graphical AbstractWe show that ATP and its ligand-gated P2X receptors are essential signaling components within both the chemosensory systems and the unique bioenergetic center, present in the CNS of the sea slugAplysia californica– a prominent model in neuroscience. Expression and pharmacology of P2X receptors inAplysiaconfirms the preservation of evolutionary conserved bioenergetic sensors across animals and provide new tools to decipher homeostatic mechanisms in neuro-endocrine systems in general.
Early birds, late owls, and the ecological role of intra-population chronotype variation
Authors: Royzrakh-Pasternak Ella , Dayan Tamar , Levy Ofir , Kronfeld-Schor Noga 
Published: August 2020

AbstractWhile the molecular mechanisms underlying variation in chronotypes within populations have been studied extensively, the ultimate selective forces governing it are poorly understood. The proximate cause is variation in clock genes and protein expression, which produces variation in tau (period length of the circadian clock), with early individuals having shorter tau. We studied within-population variation in foraging activity times of twoAcomysspecies in the field. This variation manifested in a regular and consistent sequence of individual foraging activity that is positively and strongly correlated with variation in tau. Thus, variation in circadian clock period length (tau) appears to be the mechanism underlying the regular pattern of intraspecific temporal partitioning. Late chronotypes also spent more time torpid than earlier ones, suggesting an energetic cost to this strategy and possible tradeoffs. We suggest that variation in tau is an adaptive mechanism to reduce competition between individuals within a population.
Non-invasive brain-spine interface: continuous brain control of trans-spinal magnetic stimulation using EEG
Authors: Insausti-Delgado Ainhoa , López-Larraz Eduardo , Nishimura Yukio , Ziemann Ulf , Ramos-Murguialday Ander 
Published: August 2020

AbstractBrain-controlled neuromodulation therapies have emerged as a promising tool to promote functional recovery in patients with motor disabilities. This neuromodulatory strategy is exploited by brain-machine interfaces and could be used for restoring lower limb muscle activity or alleviating gait deficits. Towards a non-invasive approach for leg neurorehabilitation, we present a set-up that combines acquisition of electroencephalographic (EEG) activity to volitionally control trans-spinal magnetic stimulation (ts-MS). We engineered, for the first time, a non-invasive brain-spine interface (BSI) to contingently connect motor cortical activation during leg motor imagery with the activation of leg muscles via ts-MS. This novel brain-controlled stimulation was validated with 10 healthy participants who underwent one session including different ts-MS conditions. After a short screening of their cortical activation during lower limb motor imagery, the participants used the closed-loop system at different stimulation intensities and scored system usability and comfort. We demonstrate the efficiency and robustness of the developed system to remove online stimulation artifacts from EEG regardless of ts-MS intensity used. All the participants reported absence of pain due to ts-MS and good usability. Our results also revealed that ts-MS controlled afferent and efferent intensity-dependent modulation of the nervous system. The here presented system represents a novel non-invasive means to neuromodulate peripheral nerve activity of lower limb using brain-controlled spinal stimulation.
A UropathogenicE. coliUTI89 model of prostatic inflammation and collagen accumulation for use in studying aberrant collagen production in the prostate
Authors: Ruetten Hannah , Sandhu Jaskiran , Mueller Brett , Wang Peiqing , Zhang Helen L. , Wegner Kyle A. , Cadena Mark , Sandhu Simran , Abler Lisa , Zhu Jonathan , O’Driscoll Chelsea A. , Chelgren Britta , Wang Zunyi , Shen Tian , Barasch Jonathan , Bjorling Dale E. , Vezina Chad M. 
Published: August 2020

ABSTRACTBacterial infection is one known etiology of prostatic inflammation. Prostatic inflammation is associated with prostatic collagen accumulation and both are linked to progressive lower urinary tract symptoms in men. We characterized a model of prostatic inflammation utilizing transurethral instillations ofE. coliUTI89 in C57BL/6J male mice with the goal of determining the optimal instillation conditions, understanding the impact of instillation conditions on urinary physiology, and identifying ideal prostatic lobes and collagen 1a1 prostatic cell types for further analysis. The smallest instillation volume tested (50 µL) distributes exclusively to bladder, 100 and 200 µL volumes distributes to bladder and prostate, and a 500 µL volume distributes to bladder, prostate and ureter. A threshold optical density (OD) of 0.4E. coliUTI89 in the instillation fluid is necessary for significant (p < 0.05) prostate colonization.E. coliUTI89 infection results in a low frequency, high volume spontaneous voiding pattern. This phenotype is due to exposure toE. coliUTI89, not catheterization alone, and is minimally altered by a 50 µL increase in instillation volume and doubling ofE. coliconcentration. Prostate inflammation is isolated to the dorsal prostate and is accompanied by increased collagen density. This is partnered with increased density of PTPRC+, ProCOL1A1+ co-positive cells and decreased density of ACTA2+, ProCOL1A1+ co-positive cells. Overall, we determined that this model is effective in altering urinary phenotype and producing prostatic inflammation and collagen accumulation in mice.