bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of Right Upper Quadrant Ultrasound in Estimating Gallbladder Wall Thickness
Authors: Cefalu Lindsay , McMurray Robert , Sizemore Grant , Bieniek Gerald , Lustik Michael , Yheulon Christopher 
Published: December 2018

Objective:
Ultrasound (US) evaluation of biliary pathology can be influenced by a variety of factors. This study examines the effect of patient specific factors on the accuracy of sonographic evaluation of gallbladder wall thickness (GBW).

Methods:
We performed a retrospective review of all patients who underwent cholecystectomy at a single institution from November 2012 to October 2015. GBW measured on US was compared with pathology results. Results were analyzed in relation to patient specific factors to include BMI, age, presence of diabetes, sex, and urgent versus elective cases.

Results:
In total 601 patients underwent cholecystectomy, 484 of which had paired preoperative US GBW measurement and postoperative pathologic specimen measurement. No significant difference in accuracy or precision of US measurement of the GBW based on BMI was found. Accuracy was not related to age, sex, urgency, or diabetes. Precision decreased with pathologic thickening, age, male sex, and urgent case performance.

Conclusions:
US is accurate in measuring GB wall thickness regardless of patient specific factors. A nonsignificant trend exists with decreased precision with pathologic thickening, age, male sex, and urgently performed cases.
Laparoscopic Multiple Parenchyma-sparing Concomitant Liver Resections for Colorectal Liver Metastases
Authors: Kazaryan Airazat M. , Aghayan David L. , Barkhatov Leonid I. , Fretland Åsmund A. , Edwin Bjørn 
Published: December 2018

Background:
Parenchyma-sparing concept in liver surgery has received a new incitement with the introduction of laparoscopic techniques. Multiple concomitant liver resections are a major component in the parenchyma-sparing concept.

Materials and Methods:
In total, 689 patients underwent laparoscopic liver resection for colorectal liver metastases from August 1998 to 2017, and 171 patients were eligible for this study. Patients were divided into 3 groups: group I with single liver resection (36 patients); group II with multiple concomitant liver resections (104 patients); group III with liver resection(s) combined with concomitant liver ablation (31 patients). Perioperative outcomes and survival were compared between the groups I and II, whereas variables of group III were presented as complementary information, avoiding statistically exigent multiple comparisons.

Results:
There were 6 conversions, 0, 3 (2.9%), and 2 (6.5%), respectively in the groups I, II, and III. Median operative time was 161, 186, and 224 minute in the groups I, II, and III, respectively. Median blood loss was 300 mL in groups I and II, and 200 mL in group III. It was a tendency to higher rate of postoperative complications in the group of single resections with morbidity rate of 31%, 19%, and 23% in group I, II, and III, respectively. Median postoperative stay was 3 days in all groups. Tumor-free margin resection was achieved in 92%, 86%, and 93%, respectively in the groups I, II, III. The median weight of resected specimen was significantly lower in group II (90 vs. 257 g; P<0.001). There were no significant differences in survival between the groups. The 5-year overall survival was 31%, 42%, and 43% for groups I, II, and III, respectively.

Conclusions:
Laparoscopic multiple concomitant parenchyma-sparing liver resections provide surgical and oncologic outcomes comparable with single greater resections for multiple lesions. This approach could be recommended for a wide application in specialized hepatopancreatobiliary centers.
Low Bladder Compliance in Women: A Clinical Overview
Authors: Arunachalam Divya , Heit Michael 
Published: December 2018

Abstract
Bladder compliance refers to the ability of the bladder to accommodate large volumes of urine. Patients with low bladder compliance may present with persistent urinary incontinence and/or evidence of upper tract damage. Clinicians often may not consider low bladder compliance in their differential for patients complaining of bothersome lower urinary tract symptoms. In this article, we aim to provide further guidance in the management of women with low bladder compliance given the lack of information on this topic in the medical literature.
Methods of conservative antibiotic treatment of acute uncomplicated appendicitis: A systematic review
Authors: Talan David A. , Saltzman Darin J. , DeUgarte Daniel A. , Moran Gregory J. 
Published: December 2018

BACKGROUND
Meta-analyses and a recent guideline acknowledge that conservative management of uncomplicated appendicitis with antibiotics can be successful for patients who wish to avoid surgery. However, guidance as to specific management does not exist.

METHODS
PUBMED and EMBASE search of trials describing methods of conservative treatment was conducted according to Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines.

RESULTS
Thirty-four studies involving 2,944 antibiotic-treated participants were identified. The greatest experience with conservative treatment is in persons 5 to 50 years of age. In most trials, imaging was used to confirm localized appendicitis without evidence of abscess, phlegmon, or tumor. Antibiotics regimens were generally consistent with intra-abdominal infection treatment guidelines and used for a total of 7 to 10 days. Approaches ranged from 3-day hospitalization on parenteral agents to same-day hospital or ED discharge of stable patients with outpatient oral antibiotics. Minimum time allowed before response was evaluated varied from 8 to 72 hours. Although pain was a common criterion for nonresponse and appendectomy, analgesic regimens were poorly described. Trials differed in use of other response indicators, that is, white blood cell count, C-reactive protein, and reimaging. Diet ranged from restriction for 48 hours to as tolerated. Initial response rates were generally greater than 90% and most participants improved by 24 to 48 hours, with no related severe sepsis or deaths. In most studies, appendectomy was recommended for recurrence; however, in several, patients had antibiotic retreatment with success.

CONCLUSION
While further investigation of conservative treatment is ongoing, patients considering this approach should be advised and managed according to study methods and related guidelines to promote informed shared decision-making and optimize their chance of similar outcomes as described in published trials. Future studies that address biases associated with enrollment and response evaluation, employ best-practice pain control and antibiotic selection, better define cancer risk, and explore longer time thresholds for response, minimized diet restriction and hospital stays, and antibiotic re-treatment will further our understanding of the potential effectiveness of conservative management.

LEVEL OF EVIDENCE
Systematic review, level II.
Kidney Discard Rates in the United States During American Transplant Congress Meetings
Authors: Abdelwahab Elhamahmi Dina , Chaly Thomas , Wei Guo , Hall Isaac E. 
Published: December 2018

Background
Deceased-donor kidney discard rates vary by region, but it is unknown whether discard rates and transplant outcomes vary during the American Transplant Congress (ATC) each year.

Methods
Using national registry data, we determined rates of kidney discard, delayed graft function, graft failure, and mortality from December 31, 1999, through December 30, 2015, during ATC dates and compared these rates with those on the same days of the week during the 2 weeks before and after the ATC (non-ATC). We used multivariable regression to determine associations between ATC and these outcomes.

Results
From 7902 donors (1575 ATC; 6327 non-ATC), 12 588 recipients received kidney transplants (2455 ATC; 10 133 non-ATC), and 2666 kidneys were discarded (582 ATC; 2084 non-ATC). Kidneys were more often discarded during ATC (19% vs 17%, P = 0.006; adjusted odds ratio, 1.21; 95% confidence interval, 1.05-1.40). There were no significant differences in donor, transplant, or recipient characteristics by ATC/non-ATC dates or by ATC/non-ATC transplant dates for delayed graft function, graft failure, or mortality.

Conclusions
On the basis of a 21% increased odds of discard, the ATC itself may result in 5 additional kidney discards during this important conference every year, which suggests the need for innovative staffing or other logistic solutions during these planned meetings.
Diagnostic error and neuro-ophthalmology
Authors: Stunkel Leanne , Newman Nancy J. , Biousse Valérie 
Published: December 2018

Purpose of review
This review summarizes the recent literature on diagnostic error relevant to the practice of neuro-ophthalmology, and evaluates the potential for increased access to neuro-ophthalmology to decrease rates of diagnostic error, thereby reducing medical harm and spending on unnecessary tests and treatments.

Recent findings
Despite medical advances, current research continues to show alarmingly high rates of diagnostic error. Research into diagnostic error shows that many of these errors can be traced to cognitive errors. Recent studies on diagnostic problems relevant to neuro-ophthalmology, including studies of misdiagnosis of posterior communicating artery aneurysms, idiopathic intracranial hypertension, optic neuritis, and optic nerve sheath meningiomas, have identified major causes of diagnostic error in these conditions.

Summary
Studies on diagnostic error in neuro-ophthalmologic conditions show that prior to evaluation by a neuro-ophthalmologist, patients may undergo unnecessary tests and treatments that are costly and potentially harmful. Further research on diagnostic error will inform better utilization of neuro-ophthalmologists as a resource to decrease diagnostic error.
Management of patients with unruptured intracranial aneurysms
Authors: Rinkel Gabriel J.E. 
Published: December 2018

Purpose of review
Intracranial aneurysms are frequent incidental findings on cranial imaging. The decision for preventive treatment depends on the presumed risk of rupture, the efficacy and risk of complications of preventive treatment, and the quality of life having to live with an unruptured aneurysms. Data on all these factors are still incomplete, and additional data are needed.

Recent findings
The current review describes advances of the last 2 years in assessment of risk of rupture, on risks of preventive aneurysms occlusion, on follow-up imaging and on medical management of patients with unruptured intracranial aneurysms.

Summary
In addition to risk factors used to predict absolute risks of rupture, also aneurysm irregularity and aneurysm growth during follow-up are potential risk factors for rupture. To what extent these factors improve risk prediction in absolute terms is yet uncertain. Uncertainty also continues on whether endovascular or surgical occlusion is the preferred method, but a trial comparing these two strategies is ongoing. Aneurysm growth can now be predicted in absolute risks. Enhancement of the aneurysm wall on MRI probably is also related to aneurysm instability and reflects inflammation. A trial assessing the effects of anti-inflammatory treatment and blood pressure lowering on aneurysm growth and rupture is currently ongoing.
GA-repeats on mammalian X chromosomes support Ohno’s hypothesis of dosage compensation by transcriptional upregulation
Authors: D’Souza Edridge , Hosage Elizaveta , Weinand Kathryn , Gisselbrecht Steve , Markstein Vicky , Markstein Peter , Bulyk Martha L. , Markstein Michele 
Published: December 2018

ABSTRACTOver 50 years ago, Susumo Ohno proposed that dosage compensation in mammals would require upregulation of gene expression on the single active X chromosome, a mechanism which to date is best understood in the fruit fly Drosophila melanogaster. Here, we report that the GA-repeat sequences that recruit the conserved MSL dosage compensation complex to the Drosophila X chromosome are also enriched across mammalian X chromosomes, providing genomic support for the Ohno hypothesis. We show that mammalian GA-repeats derive in part from transposable elements, suggesting a mechanism whereby unrelated X chromosomes from dipterans to mammals accumulate binding sites for the MSL dosage compensation complex through convergent evolution, driven by their propensity to accumulate transposable elements.
Co-opted transposons help perpetuate conserved higher-order chromosomal structures
Authors: Choudhary Mayank NK , Friedman Ryan Z , Wang Julia T , Jang Hyo Sik , Zhuo Xiaoyu , Wang Ting 
Published: December 2018

ABSTRACTTransposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include architectural proteins—such as CTCF, RAD21 and SMC3—that are involved in tethering chromatin loops and marking domain boundaries. The 3D organization of the mammalian genome is intimately linked to its function and is remarkably conserved. However, the mechanisms by which these structural intricacies emerge and evolve have not been thoroughly probed. Here we show that TEs contribute extensively to both the formation of species-specific loops in humans and mice via deposition of novel anchoring motifs, as well as to the maintenance of conserved loops across both species via CTCF binding site turnover. The latter function demonstrates the ability of TEs to contribute to genome plasticity and reinforce conserved genome architecture as redundant loop anchors. Deleting such candidate TEs in human cells leads to a collapse of such conserved loop and domain structures. These TEs are also marked by reduced DNA methylation and bear mutational signatures of hypomethylation through evolutionary time. TEs have long been considered a source of genetic innovation; by examining their contribution to genome topology, we show that TEs can contribute to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture globally, revealing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation.One-sentence summaryCo-option of transposable elements maintains conserved 3D genome structures via CTCF binding site turnover in human and mouse.
Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa
Authors: Tanabe Yuuhiko , Yamaguchi Haruyo 
Published: December 2018

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.
Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome
Authors: Voges Mathias J.E.E.E. , Bai Yang , Schulze-Lefert Paul , Sattely Elizabeth S. 
Published: December 2018

SignificanceThe root microbiome composition is largely determined by the soil inoculum, with a distinct contribution from the host. Yet, the molecular mechanisms with which the host influences its rhizobiome are only beginning to be discovered. Using a hydroponics-based synthetic community approach, we probe the impact of root-exuded specialized metabolites in shaping the root microbiome. We uncover a role for coumarins in structuring the rhizobiome, particularly by limiting the growth of a Pseudomonas strain, for which we propose a mechanism of action. Our findings support the exciting possibility that root-exuded coumarins form a part of the plant’s adaptive response to iron deficiency that goes beyond iron mobilization to modulate the rhizobiome, and highlights avenues towards engineering the rhizosphere for plant health.AbstractThe factors that dictate the composition of the root microbiome and its role in plant fitness has been a long-standing question. Recent work has highlighted a major contribution of the soil inoculum in determining the composition of the root microbiome. However, plants are known to conditionally exude a diverse array of unique secondary metabolites, largely varying between species and environmental conditions. Here, we explore the role of specialized metabolites in dictating which bacteria reside in the rhizosphere. We employed a reduced synthetic community (SynCom) of Arabidopsis thaliana root-isolated bacteria to detect community shifts that occur in the absence of the secreted small molecule phytoalexins, flavonoids, and coumarins. We find that lack of coumarin biosynthesis in f6’h1 mutant plant lines causes a shift in the root microbial community specifically under iron deficiency. We demonstrate a potential role for iron-mobilizing coumarins in sculpting the A. thaliana root bacterial community by inhibiting the proliferation of a relatively abundant Pseudomonas species via a redox-mediated mechanism. This work establishes a systematic approach enabling elucidation of specific mechanisms by which plant-derived molecules mediate microbial community composition. Our findings expand on the function of conditionally-exuded specialized metabolites and lead to new avenues to effectively engineer the rhizosphere for improving crop growth in alkaline soils, which make up a third of total arable soils.
Extreme genetic signatures of local adaptation during plant colonization
Authors: Shah Niraj , Wakabayashi Tomomi , Kawamura Yasuko , Skovbjerg Cathrine Kiel , Wang Ming-Zhuo , Mustamin Yusdar , Isomura Yoshiko , Gupta Vikas , Jin Haojie , Mun Terry , Sandal Niels , Azuma Fuyuki , Fukai Eigo , Seren Ümit , Kusakabe Shohei , Kikuchi Yuki , Nitanda Shogo , Kumaki Takashi , Sønderkær Mads , Nielsen Kaare Lehmann , Schneeberger Korbinian , Stougaard Jens , Sato Shusei , Schierup Mikkel Heide , Andersen Stig Uggerhøj 
Published: December 2018

AbstractColonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with the recent colonization of Japan byLotus japonicus. We carefully track the colonization process whereL. japonicusgradually spread from subtropical conditions to much colder climates in northern Japan. We characterize the loss of diversity during this process and identify genomic regions with extreme genetic differentiation. Next, we perform population structure-corrected association mapping of phenotypic traits measured in a common garden and discover a number of genome-wide significant associations. Contrasting these analyses, we find that there is a strong concordance between phenotypic variation and extreme differentiation for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection by local adaptation during the colonization process and point to associated candidate genes.
Gene augmentation and read-through rescue channelopathy in an iPSC-RPE model of congenital blindness
Authors: Shahi Pawan K. , Hermans Dalton , Sinha Divya , Brar Simran , Moulton Hannah , Stulo Sabrina , Borys Katarzyna D. , Capowski Elizabeth , Pillers De-Ann M. , Gamm David M. , Pattnaik Bikash. R. 
Published: December 2018

PurposeMutations in the KCNJ13 gene are known to cause Leber’s Congenital Amaurosis (LCA16), an inherited pediatric blindness. KCNJ13 gene encodes the Kir7.1 subunit protein which acts as a tetrameric inwardly rectifying potassium ion channel in the retinal pigment epithelium to maintain ionic homeostasis thereby allowing photoreceptors to encode visual information. We sought to determine if genetic approaches might be effective in treating blindness due to mutations in KCNJ13.MethodsWe developed patient-derived hiPSC-RPE carrying an autosomal recessive nonsense mutation in the KCNJ13 gene (c.158G>A, p.Trp53*). We performed biochemical and electrophysiology assays of Kir7.1 function. Both small molecule read-through drug and gene-therapy approaches were tested using this disease-in-a-dish approach.ResultsWe found that the LCA16 hiPSC-RPE had normal morphology but did not express a functional Kir7.1 channel and was unable to demonstrate normal physiology. Following read-through drug treatment, the LCA16 hiPSC cells were hyperpolarized by 30 mV and Kir7.1 current was restored. Similarly, loss-of-function of Kir7.1 channel was circumvented by lentiviral gene delivery to the hiPSC-RPE cells. In either approach, Kir7.1 protein was expressing normally with restoration of membrane potential and Kir7.1 current.ConclusionLoss-of-function mutation in Kir7.1 is a cause of LCA. Using either read-through therapy or gene augmentation, we rescued Kir7.1 channel function in patient-derived iPSC-RPE cells via a precision medicine approach.