bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraining the climate and ocean pH of the early Earth with a geological carbon cycle model
Authors: Krissansen-Totton Joshua , Arney Giada N. , Catling David C. 
Published: April 2018

SignificanceThe climate and ocean pH of the early Earth are important for understanding the origin and early evolution of life. However, estimates of early climate range from below freezing to over 70 °C, and ocean pH estimates span from strongly acidic to alkaline. To better constrain environmental conditions, we applied a self-consistent geological carbon cycle model to the last 4 billion years. The model predicts a temperate (0–50 °C) climate and circumneutral ocean pH throughout the Precambrian due to stabilizing feedbacks from continental and seafloor weathering. These environmental conditions under which life emerged and diversified were akin to the modern Earth. Similar stabilizing feedbacks on climate and ocean pH may operate on earthlike exoplanets, implying life elsewhere could emerge in comparable environments.
Complete biosynthesis of noscapine and halogenated alkaloids in yeast
Authors: Li Yanran , Li Sijin , Thodey Kate , Trenchard Isis , Cravens Aaron , Smolke Christina D. 
Published: April 2018

Significance
We demonstrate yeast’s capacity for biosynthesis of complex plant natural products by reconstructing a de novo noscapine biosynthetic pathway and optimizing noscapine production toward scalable manufacturing. Engineered strain contains 25 heterologous plant, bacteria, and mammalian genes and 6 mutant or overexpressed yeast genes. The noscapine biosynthetic pathway incorporates seven endomembrane-localized plant enzymes, highlighting yeast’s ability to functionally express and properly localize large numbers of heterologous enzymes into the endoplasm reticulum. Noscapine titers were improved by 18,000-fold (to low mg/L levels) via a combination of enzyme engineering, pathway and strain engineering, and fermentation optimization. We demonstrated that microbial fermentation can be used to produce halogenated alkaloid derivatives, which can ultimately serve as potential drug leads, through feeding amino acid derivatives to strains.
Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane
Authors: Snyder Benjamin E. R. , Böttger Lars H. , Bols Max L. , Yan James J. , Rhoda Hannah M. , Jacobs Ariel B. , Hu Michael Y. , Zhao Jiyong , Alp E. Ercan , Hedman Britt , Hodgson Keith O. , Schoonheydt Robert A. , Sels Bert F. , Solomon Edward I. 
Published: April 2018

Significance
Understanding the structure of iron active sites that form in zeolites is critical to understanding the extreme reactivity of Fe-zeolite catalysts, which show promise in important industrial applications. This study defines the geometric structure of an Fe-zeolite active site that cleaves the inert C–H bond of methane at room temperature to form methanol. The high reactivity of this site derives from a constrained coordination geometry enforced by the rigid matrix of the catalyst. This insight into the relationship between catalyst structure and function is an important step toward cost-effective methanol fuels and chemical feedstocks derived from natural gas.
Distinct MHC class I-like interacting invariant T cell lineage at the forefront of mycobacterial immunity uncovered inXenopus
Authors: Edholm Eva-Stina , Banach Maureen , Hyoe Rhoo Kun , Pavelka Martin S. , Robert Jacques 
Published: April 2018

SignificanceContrasting with the dominance of conventional adaptive T cells in adult frogs,Xenopustadpoles prominently rely on innate-like T (iT) cells expressing invariant TCRα rearrangements to combat pathogens. Here, we use three complementary loss-of-function approaches combining RNA interference with transgenesis or CRISPR/Cas9 genome editing to unveil an ancestral antimycobacterial immune surveillance system represented by MHC-like interacting innate-like T cells. Notably, this MHC-like (XNC4)/iVα45T cell system is critical for host defense against mycobacteria and distinctive from the key antiviral MHC-like XNC10-restricted iVα6T cells previously identified. These findings imply diversification and specialization of an ancestral innate-like T cell recognition system that is evolutionarily convergent to that of mammals.
Molecular excitonic seesaws
Authors: Wilhelm Philipp , Schedlbauer Jakob , Hinderer Florian , Hennen Daniel , Höger Sigurd , Vogelsang Jan , Lupton John M. 
Published: April 2018

Significance
Transformation of light into electronic excitation energy and the spatial redistribution of this energy within a complex of molecular units constitute the processes central to photochemical energy conversion in photosynthesis. Excitations migrate downward in energy between molecules, ultimately localizing at a global energetic minimum. But, how does energy flow in a system with built-in bistability, a local and a global energetic minimum? A molecular excitonic seesaw structure probes such fundamental intramolecular bistability. Much like watching a pen balanced on its tip fall randomly, in single molecules, energy flows nondeterministically to one or the other energetic minimum. Such a labile excitonic seesaw makes energy transfer highly susceptible to external stimuli and can be controlled, for example, by the incident light polarization.
Multiple nuclear-replicating viruses require the stress-induced protein ZC3H11A for efficient growth
Authors: Younis Shady , Kamel Wael , Falkeborn Tina , Wang Hao , Yu Di , Daniels Robert , Essand Magnus , Hinkula Jorma , Akusjärvi Göran , Andersson Leif 
Published: April 2018

Significance
There is a strong need for the development of new antiviral therapies, and this study sheds light on a host–virus interaction that is significant for a number of medically important human viruses. The study also suggests that the RNA-binding zinc finger CCCH-type containing 11A (ZC3H11A) protein takes part in a mechanism that facilitates nuclear export of mRNA, particularly under cellular stress, a mechanism that has been “hijacked” by several nuclear-replicating viruses to promote their replication. ZC3H11A is therefore a potential target for development of an antiviral therapy.
Draft genome of the Peruvian scallop Argopecten purpuratus
Authors: Li Chao , Liu Xiao , Liu Bo , Ma Bin , Liu Fengqiao , Liu Guilong , Shi Qiong , Wang Chunde 
Published: April 2018

Abstract

Background
The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops.

Findings
A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly.

Conclusions
We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.
A practical tool for maximal information coefficient analysis
Authors: Albanese Davide , Riccadonna Samantha , Donati Claudio , Franceschi Pietro 
Published: April 2018

Abstract

Background
The ability of finding complex associations in large omics datasets, assessing their significance, and prioritizing them according to their strength can be of great help in the data exploration phase. Mutual information-based measures of association are particularly promising, in particular after the recent introduction of the TICe and MICe estimators, which combine computational efficiency with superior bias/variance properties. An open-source software implementation of these two measures providing a complete procedure to test their significance would be extremely useful.

Findings
Here, we present MICtools, a comprehensive and effective pipeline that combines TICe and MICe into a multistep procedure that allows the identification of relationships of various degrees of complexity. MICtools calculates their strength assessing statistical significance using a permutation-based strategy. The performances of the proposed approach are assessed by an extensive investigation in synthetic datasets and an example of a potential application on a metagenomic dataset is also illustrated.

Conclusions
We show that MICtools, combining TICe and MICe, is able to highlight associations that would not be captured by conventional strategies.
Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building
Authors: Pomerantz Aaron , Peñafiel Nicolás , Arteaga Alejandro , Bustamante Lucas , Pichardo Frank , Coloma Luis A , Barrio-Amorós César L , Salazar-Valenzuela David , Prost Stefan 
Published: April 2018

Abstract

Background
Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here, we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack in one of the world's most imperiled biodiversity hotspots, the Ecuadorian Chocó rainforest. We used portable equipment, including the MinION nanopore sequencer (Oxford Nanopore Technologies) and the miniPCR (miniPCR), to perform DNA extraction, polymerase chain reaction amplification, and real-time DNA barcoding of reptile specimens in the field.

Findings
We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of &gt;99% in less than 24 hours after collecting specimens. The flexibility of our mobile laboratory further allowed us to generate sequence information at the Universidad Tecnológica Indoamérica in Quito for rare, endangered, and undescribed species. This includes the recently rediscovered Jambato toad, which was thought to be extinct for 28 years. Sequences generated on the MinION required as few as 30 reads to achieve high accuracy relative to Sanger sequencing, and with further multiplexing of samples, nanopore sequencing can become a cost-effective approach for rapid and portable DNA barcoding.

Conclusions
Overall, we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas to aid in conservation efforts and be applied to research facilities in developing countries. This opens up possibilities for biodiversity studies by promoting local research capacity building, teaching nonspecialists and students about the environment, tackling wildlife crime, and promoting conservation via research-focused ecotourism.
Does Day of Surgery Affect Hospital Length of Stay and Charges Following Minimally Invasive Transforaminal Lumbar Interbody Fusion?
Authors: Hijji Fady Y. , Narain Ankur S. , Haws Brittany E. , Khechen Benjamin , Kudaravalli Krishna T. , Yom Kelly H. , Singh Kern 
Published: April 2018

Study Design:
Retrospective Cohort.

Objective:
To determine if an association exists between surgery day and length of stay or hospital costs after minimally invasive transforaminal lumbar interbody fusion (MIS TLIF).

Summaryof Background Data:
Length of inpatient stay after orthopedic procedures has been identified as a primary cost driver, and previous research has focused on determining risk factors for prolonged length of stay. In the arthroplasty literature, surgery performed later in the week has been identified as a predictor of increased length of stay. However, no such investigation has been performed for MIS TLIF.

Materials and Methods:
A surgical registry of patients undergoing MIS TLIF between 2008 and 2016 was retrospectively reviewed. Patients were grouped based on day of surgery, with groups including early surgery and late surgery. Day of surgery group was tested for an association with demographics and perioperative variables using the student t test or χ2 analysis. Day of surgery group was then tested for an association with direct hospital costs using multivariate linear regression.

Results:
In total, 438 patients were analyzed. In total, 51.8% were in the early surgery group, and 48.2% were in the late surgery group. There were no differences in demographics between groups. There were no differences between groups with regard to operative time, intraoperative blood loss, length of stay, or discharge day. Finally, there were no differences in total hospital charges between early and late surgery groups (P=0.247).

Conclusions:
The specific day on which a MIS TLIF procedure occurs is not associated with differences in length of inpatient stay or total hospital costs. This suggests that the postoperative course after MIS TLIF procedures is not affected by the differences in hospital staffing that occurs on the weekend compared with weekdays.
Conservative Treatment of Hangman Variant Fractures
Authors: Niemeier Thomas E. , Manoharan Sakthevil R. , Mukherjee Amrita , Theiss Steven M. 
Published: April 2018

Study Design:
This is retrospective cohort study.

Objective:
Investigate the stability of patients with hangman variant fractures and outcomes of treatment with external immobilization.

Summary of Background Data:
Traumatic spondylolisthesis of the axis (C2) with the fracture extending into the vertebral body has been incompletely characterized. Small case series have showed high rates of neurological injury and cite difficulty treating closed due to greater instability secondary to extensive ligamentous injury.

Materials and Methods:
Retrospectively, all patients admitted to a level 1 trauma center from 2004 to 2015 with acute C2 fractures were identified and classified based on computed tomographic imaging. Study cohort included patients with anterior translation <5 mm and C2–3 angulation <15 degrees that were followed to conclusion of treatment.

Results:
In total, 107 hangman’s variant fractures (14.5%) were identified from a database of 735 acute C2 fractures. In total, 106 of the 107 patients displayed no neurological injury related to the cervical spine at the time of presentation. A total of 63 patients met the inclusion criteria and were followed as outpatients until collar or halo vest removal. All fractures progressed to union without progressive displacement or late neurological injury. No difference was observed in radiographic outcome between patients treated in a hard collar versus halo orthosis.

Conclusions:
Although widely considered a difficult fracture to treat with closed means, hangman variants are relatively neurologically benign injuries with low incidence of ligamentous injury. Fractures with <5 mm of horizontal translation and 15 degrees of angulation can be treated with external immobilization. Our results suggest no advantage of halo immobilization versus hard collar orthosis.
Latexin and hematopoiesis
Authors: Zhang Cuiping , Liang Ying 
Published: April 2018

Purpose of review
Hematopoietic stem cells (HSCs) produce mature blood cells throughout lifetime. Natural genetic diversity offers an important yet largely untapped reservoir for deciphering regulatory mechanisms of HSCs and hematopoiesis. In this review, we explore the role of latexin, identified by natural variation, in regulating homeostatic and stress hematopoiesis, unravel the underlying signaling pathways, and propose its therapeutic implication.

Recent findings
Latexin acts endogenously in HSCs to negatively regulate their population size by enhancing apoptosis and by decreasing self-renewal. Deletion of latexin in vivo increases HSC repopulation capacity and survival, expands the entire hematopoietic system, and mitigates myelosuppression. Latexin inactivation downregulates thrombospondin 1 (Thbs1). It inhibits nuclear translocation of ribosomal protein subunit 3 (Rps3), a novel latexin-binding protein, and sensitizes hematopoietic cells to radiation-induced cell death. However, how latexin-Rps3 pathway regulates Thbs1 transcription is unclear. Latexin is downregulated in cancer cells because of promoter hypermethylation, but latexin-depleted mice do not inherently develop hematologic malignancies even with aging. The mechanism of action of latexin in tumorigenesis remains largely unknown.

Summary
Understanding how latexin regulates HSC survival, self-renewal, and stress response will advance our knowledge of HSC biology. It will facilitate the development of a novel therapeutic strategy for hematopoietic regeneration and cancer treatment.
HIV Testing With and Without a Clinical Consultation Among Men Who Have Sex With Men: A Randomized Controlled Trial
Authors: Read Tim R. H. , Walker Sandra , Chow Eric P. F. , Ong Jason J. , Bradshaw Catriona S. , Medland Nick A. , Wigan Rebecca , Chen Marcus Y. , Fairley Christoper K. 
Published: April 2018

Background:
Increasing the frequency of HIV testing among men who have sex with men (MSM) maximizes the preventive effect of antiretroviral therapy, by reducing time to diagnosis and treatment.

Setting:
Melbourne Sexual Health Centre, Australia.

Methods:
This randomized controlled trial evaluated whether access to testing, without seeing a clinician would increase testing frequency. MSM attending for HIV testing between July 2014 and April 2015 were randomized in 1:1 ratio to the intervention arm (access to HIV and syphilis testing at 300 pathology centers, without requiring consultations) or the control arm (consultation at every test), without blinding. The primary outcome was the incidence of HIV testing over 12 months.

Results:
Of 443 men referred, 422 were randomized, 3 HIV positives at baseline were excluded, and 419 were analyzed. Of 208 control, 202 (97.1%) and 200 (94.8%) of 211 intervention group members were followed to 12 months. The intervention group had 453 tests in 205.6 person-years, incidence rate was 2.2 (95% confidence interval [CI]: 2.0 to 2.4) tests per year. The control group had 432 tests during 204.0 person-years, incidence rate was 2.1 (95% CI: 1.9 to 2.3) tests per year, and incidence rate ratio was 1.04 (95% CI: 0.89 to 1.2; P = 0.63). The annual rate of consultations was as follows: intervention, 1.61 (95% CI: 1.44 to 1.79); controls, 2.12 (95% CI: 1.92 to 2.33); rate ratio, 0.76 (95% CI: 0.65 to 0.88; P = 0.0001). There was no difference in quality of life scores (P = 0.61).

Conclusions:
MSM permitted HIV and syphilis testing outside of clinical consultations did not test more frequently than controls but had 24% fewer consultations, reducing service demand. Trial registration: ACTRN12614000760673.
Impact of Nasal Septal Surgery on Sleep Quality and Attention-Deficit/Hyperactivity Disorder
Authors: Deveci Ildem , Onder Serap , Surmeli Mehmet , Sahin Samil , Kipoglu Betul Aktas , Karabulut Burak , Eser Basak Caypinar 
Published: April 2018

Objective:
To evaluate the effect of nasal septal surgery on quality of life.

Methods:
A total of 49 patients who underwent septoplasty and/or inferior turbinate radiofrequency operations for nasal septal deviation and inferior turbinate hypertrophy were prospectively enrolled in the study. All patients completed the adult attention-deficit/hyperactivity disorder scale (ADHD scale) and Pittsburgh sleep quality index (PSQI) before and after septoplasty. Acoustic rhinometric measurements were also recorded.

Results:
Acoustic rhinometric measurements and PSQI showed statistically significant improvement after nasal surgery (P < 0.05), but no statistically significant difference was present between pre- and postoperative ADHD scores (P > 0.05).

Conclusion:
Besides the functional improvement of septoplasty, a long-lasting improvement in the quality of life is observed in patients with that undergo this surgery.
Outcomes After Open Reduction With Internal Fixation of Mandible Fractures
Authors: Barry Rahman G. , Wolbert Thao T. , Gress Todd W. , Ray Peter D. , Mozaffari Farid B. 
Published: April 2018

Introduction/Hypothesis:
Mandible fractures contribute substantially to morbidity after blunt trauma. Controversy exists surrounding the appropriate timing of surgical intervention and benefit from routine postreduction imaging.

Methods:
The authors retrospectively reviewed 146 patients who sustained traumatic mandible fractures at a level 2 trauma center over a 5-year period, between January 2012 and December 2016. The authors excluded all patients who did not undergo surgery, underwent operative closed reduction only, sustained other significant maxillofacial injuries, penetrating mechanisms, and other major injuries based on injury severity scores (ISS) over 15. There were 51 patients meeting inclusion criteria. The authors reviewed admission face computed tomography (CT) scans and Panorex x-rays. Patients were divided into early (<72 hours) and late (>72 hours) open reduction with internal fixation (ORIF) groups. The authors reviewed demographics, mechanism of injury, postreduction imaging, and ISS. All statistical analyses were performed using Stata 15.

Results:
There were 39 males (76%) and 12 females (24%) in the authors’ study, with a mean age of 32 years. Twenty-eight patients (55%) underwent early ORIF and 23 patients (45%) underwent late ORIF, with no mortalities. There was no statistically significant difference in ISS between the 2 groups (P = 0.081). Preoperative face CT scans were performed in 49 patients (96%) and Panorex in 2 patients (4%). Eight patients (16%) had both modalities, with CT face identifying fractures in 5 patients not seen on Panorex, resulting in a change in operative approach. Postreduction imaging was obtained in 33 patients (65%), of whom 26 were Panorex X-rays. These demonstrated adequate reduction in 31 patients (94%) and did not change management in any instance. Complications occurred in 19 patients (37%), of whom there were 11 with uncontrolled pain after 1 week, 6 abscesses, 5 nonunions/malunions, 2 hardware extrusions, and 1 incisional dehiscence. A positive urine drug screen predicted uncontrolled pain (P < 0.05). There was no statistically significant difference in complications between the 2 groups.

Conclusion:
The authors’ data suggest that CT scans of the face are superior to panoramic radiographs in traumatic mandible fracture evaluation, with no apparent benefit from routine postreduction imaging in detecting complications. Open reduction with internal fixation remains an effective treatment with favorable outcomes, and operative delays > 72 hours do not appear to increase complication rates.
Bilateral Post-Traumatic Facial Paralysis That Contains Longitudinal and Transverse Temporal Fracture
Authors: Şahin Caner , Özen Özkan 
Published: April 2018

Abstract
Acute bilateral post-traumatic facial paralysis is rare in the literature. Post-traumatic facial paralysis is frequently accompanied transverse fractures of temporal more. The incidence of acute bilateral post-traumatic facial paralysis has been reported as 1 to 5 per million in the literature. Trauma and concurrent facial paralysis are usually in the same subsite (right temporal bone fracture and right facial paralysis). There is one pathophysiological pattern for a single temporal bone fracture in a subsite. The authors present a bilateral isolated different pathophysiological pattern sudden onset facial paralysis in a patient herein.