bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acetonitrile as a Building Block and Reactant
Authors: Hoff B. 
Published: June 2018

Acetonitrile is popular as a solvent for performing organic reactions, as a ligand in inorganic chemistry, as a mobile phase in chromatography, and as an electrolyte solvent in dye-sensitized solar cells. This is mainly due to its ability to dissolve both polar and nonpolar components. However, acetonitrile is also a valuable building block allowing atom-efficient transformations in synthetic organic chemistry. The aim of this review is to highlight synthetic transformations using acetonitrile, covering both classical approaches and modern strategies proceeding through radical intermediates or mediated by metal catalysis. Besides showcasing synthetic protocols useful for acetonitrile and analogues, warnings for when not to use acetonitrile as a solvent are also provided.1	Introduction2	Fundamental Reactions with Acetonitrile3	Cyanomethylation of Non-Aromatics4	The Acetonitrile Nitrogen as a Nucleophile5	The Blaise Reaction6	Synthesis of Pyridines7	Other Cyclization Reactions8	Cyanomethylation of Arenes and Heteroarenes9	Acetylation of Arenes Using Acetonitrile10	Synthesis of N-Arylacetamides11	Cyanation Using Acetonitrile as a Cyanide Source12	When To Avoid Acetonitrile as a Solvent13	Conclusion
Impact of Different Aortic Entry Tear Sites on Early Outcomes and Long-Term Survival in Patients with Stanford A Acute Aortic Dissection
Authors: Merkle Julia , Sabashnikov Anton , Deppe Antje Christin , Weber Saskia , Mader Navid , Choi Yeong-Hoon , Liakopoulos Oliver , Kuhn-Régnier Ferdinand , Wahlers Thorsten 
Published: June 2018

Background Stanford A acute aortic dissection (AAD) is a life-threatening emergency. The aim of this study was to compare the impact of three different aortic entry tear sites on early outcomes and long-term survival of patients with Stanford A AAD.
Methods From January 2006 to April 2015, a total of 240 consecutive patients with diagnosed Stanford A AAD underwent emergent, isolated surgical aortic repair in our center. Patients were divided into three groups comprising isolated ascending aorta, proximal aortic arch, and distal aortic arch entry tear site and were followed up for up to 9 years.
Results Thirty-day mortality as well as major cerebrovascular events were significantly different between the three groups (p = 0.007 and p = 0.048, respectively). Overall cumulative short- and long-term survival of all patients revealed significant differences (Log-Rank p = 0.002), whereas survival of all patients free from major cerebrovascular events was similar (Log-Rank p = 0.780). Subgroup analysis of short- and long-term survival of patients showed significant differences in terms of men (Log-Rank p = 0.043), women (Log-Rank p = 0.004), patients over 65 years of age (Log-Rank p = 0.007), and hypertensive patients (Log-Rank p = 0.003). Kaplan–Meier survival estimation plots significantly showed poorest survival for distal aortic arch entry tear site group.
Conclusion The location of the primary entry tear in patients with Stanford A AAD significantly influences early outcomes, short- and long-term survival of patients, whereas survival of patients free from major cerebrovascular events showed similar results among the three groups. Distal aortic entry tear site showed poorest outcomes and survival.
Incidence of Concurrent Peroneal Nerve Injury in Multiligament Knee Injuries and Outcomes after Knee Reconstruction
Authors: Worley John R. , Brimmo Olubusola , Nuelle Clayton W. , Cook James L. , Stannard James P. 
Published: June 2018

AbstractThe purpose of this study was to determine incidence of concurrent peroneal nerve injury and to compare outcomes in patients with and without peroneal nerve injury after surgical treatment for multiligament knee injuries (MLKIs). A retrospective study of 357 MLKIs was conducted. Patients with two or more knee ligaments requiring surgical reconstruction were included. Mean follow-up was 35 months (0–117). Incidence of concurrent peroneal nerve injury was noted and patients with and without nerve injury were evaluated for outcomes. Concurrent peroneal nerve injury occurred in 68 patients (19%). In patients with nerve injury, 45 (73%) returned to full duty at work; 193 (81%) patients without nerve injury returned to full duty (p = 0.06). In patients with nerve injury, 37 (60%) returned to their previous level of activity; 148 (62%) patients without nerve injury returned to their previous level of activity (p = 0.41). At final follow-up, there were no significant differences in level of pain (mean visual analog scale 1.6 vs. 2; p = 0.17), Lysholm score (mean 88.6 vs. 88.8; p = 0.94), or International Knee Documentation Committee score (mean 46.2 vs. 47.8; p = 0.67) for patients with or without peroneal nerve injury, respectively. Postoperative range of motion (ROM) (mean 121 degrees) was significantly lower (p = 0.02) for patients with nerve injury compared with patients without nerve injury (mean 127 degrees). Concurrent peroneal nerve injury occurred in 19% of patients in this large cohort suffering MLKIs. After knee reconstruction surgery, patients with concurrent peroneal nerve injuries had significantly lower knee ROM and trended toward a lower rate of return to work. However, outcomes with respect to activity level, pain, and function were not significantly different between the two groups. This study contributes to our understanding of patient outcomes in patients with concurrent MLKI and peroneal nerve injury, with a focus on the patient's ability to return to work and sporting activity.
The Effect of Remnant Tissue Preservation in Anatomic Double-Bundle ACL Reconstruction on Knee Stability and Graft Maturation
Authors: Takahashi Tsuneari , Kimura Masashi , Hagiwara Keiichi , Ohsawa Takashi , Takeshita Katsushi 
Published: June 2018

AbstractSeveral investigators have developed anterior cruciate ligament reconstructions (ACLR) with remnant tissue preservation (RTP) and have reported better clinical outcomes. However, the effects of RTP remain controversial. To date, no reports have compared both clinical and radiological outcomes of anatomic double-bundle ACLR using the hamstring tendon and outside-in technique with/without RTP. This article evaluates the effectiveness of RTP in ACLR on knee stability and graft maturation. In total, 75 patients with unilateral ACL injury who had undergone anatomic double-bundle ACLR using autografted hamstring tendon either with RTP (Group P, n = 43) or without (Group N, n = 32) were enrolled. Clinical scores, pre- and postoperative side-to-side differences (SSDs) obtained using Telos, radiological evaluations of the grafted tendon using the signal/noise quotient (SNQ) measured using magnetic resonance imaging, and arthroscopic evaluations of the grafted tendon were retrospectively compared between the groups. Postoperative SSDs were smaller in the Group P (0.78 ± 1.90 mm) than in the Group N (1.29 ± 2.18 mm); however, this difference was not significant. Comparing two subgroups of the Group P, the SSD was significantly smaller in those with sufficient remnant coverage (−0.56 ± 1.38 mm) than in those without (1.48 ± 1.77 mm) (p = 0.019), as well as in the Group N patients (p = 0.019). The degree of synovial coverage of the anteromedial (p = 0.0064) and posterolateral (p = 0.032) bundle grafted tendon at the time of second-look arthroscopy was significantly better in the Group P than in the Group N. SNQ values of ACL grafted tendon at proximal (p = 0.049), middle, and distal (p = 0.039) one-third in Group P were better than those in Group N. RTP may enhance synovial coverage and maturation of the grafted tendon. Sufficient remnant tissue coverage may contribute to better knee stability. This is a Level III, retrospective comparative study.
Mucoid Degeneration of the Anterior Cruciate Ligament: Characterization of Natural History, Femoral Notch Width Index, and Patient Reported Outcome Measures
Authors: Hotchen Andrew J. , Demetriou Charis , Edwards Dennis , Melton Joel T. K. 
Published: June 2018

AbstractThe presentation and clinical course of mucoid degeneration of the anterior cruciate ligament (MD-ACL) are poorly documented within the literature. Subsequently, it is under-diagnosed and the optimal management strategy remains ill-defined. Here, we characterize the syndrome associated with MD-ACL and compare the natural clinical course with the outcomes of arthroscopic management. Thirty-one patients with radiological features of MD-ACL over a 2-year period had their clinical notes retrospectively reviewed. Seven patients underwent arthroscopic debridement of the ACL for MD. These were followed up for a minimum of 2 years and an average of 2.8 years from surgery. The remainder were managed conservatively (n = 24) and were followed up for a minimum of 2 years and an average of 4.0 years. The notch width index (NWI) and associated pathology was noted. Primary outcome measures were presence of knee pain and use of analgesia. Secondary outcome measures were the Oxford and Lysholm knee scores. The most commonly reported symptoms were posterior knee pain (77.4%) and limitation of terminal flexion (58.1%). All patients who underwent arthroscopic debridement were pain and analgesia free at follow-up. Of the patients who did not undergo arthroscopic surgery, three patients had knee replacement surgery and three were lost to follow-up. The remaining patients, 14/18 (77.8%), reported knee pain and regular analgesia use at follow-up, which was significantly more than the arthroscopic debridement group (p < 0.01). The knee scores were significantly better in the arthroscopic debridement group at follow-up (Oxford knee score: 45 vs 34; Lysholm: 92 vs 67; p < 0.01). Furthermore, the postoperative improvement in the Oxford knee and Lysholm scores compared with preoperatively was 12.1 and 31.8 points, respectively (p < 0.01). The NWI was increased in patients with mild-to-severe osteoarthritis (0.266 vs 0.273; p < 0.05). MD-ACL should be considered in patients who report posterior knee pain, limitation of terminal flexion, and it can be associated with other knee pathologies. MD-ACL can be successfully managed with arthroscopic radio frequency debulking with improvement in quality of life at follow-up.
Arthroscopic and 3D CT Scan Evaluation of Femoral Footprint of the Anterior Cruciate Ligament in Chronic ACL Deficient Knees
Authors: Das Anupam , Yadav C. S. , Gamanagatti Shivanand , Pandey R. M. , Mittal Ravi 
Published: June 2018

AbstractThe outcome of single-bundle anterior cruciate ligament (ACL) reconstruction depends largely on the anatomic placement of bone tunnel. The lateral intercondylar ridge (LIR) and bifurcate ridge (BR) are useful bony landmarks for femoral tunnel placement. The purpose of our study was to compare the bony landmarks of ACL footprint on femur by three-dimensional computed tomography (3D CT) scan and arthroscopy in chronic ACL-deficient knees. Fifty patients above 18 years of age who were diagnosed of having ACL tear were selected for the study. All the cases were more than 6 months old since the injury. Preoperative 3D CT scan of the affected knee was obtained for each of them. They underwent single-bundle anatomic ACL reconstruction. Measurements were done on the preoperative 3D CT and arthroscopy to quantify the position of the LIR and BR. The proximodistal distance of lateral femoral condyle was 21.41+/−2.5 mm on CT scan and 22.02+/−2.02 mm on arthroscopy. On preoperative 3D CT scan, the midpoint of the LIR was found to be located at a mean distance of 11.17±2.11 mm from the proximal margin of the lateral femoral condyle. On arthroscopy, it was at 10.18+/−1.52 mm from the proximal margin the lateral femoral condyle. The “bifurcate ridge”(BR) was not visible in any of the cases during arthroscopy or CT scan. We concluded that LIR is an easily identifiable bony landmark on arthroscopy in all cases. It can also be identified on CT scans. BR is not identified both on arthroscopy and CT scans in chronic ACL tears. The arthroscopic measurements of bony landmarks are quite close to those of CT scan. Midpoint of LIR is at 52.185% of the proximodistal distance on CT scan evaluation and it is at 46.21% on arthroscopic evaluation.
A Clinical Study of Patients with Acute Epiglottitis
Authors: Kono Michihisa , Goto Takashi , Bandoh Nobuyuki , Harabuchi Yasuaki 
Published: June 2018

AbstractAcute epiglottitis is an acute inflammation of the upper respiratory airway that rarely causes airway obstruction. A retrospective study was conducted on 115 patients with acute epiglottitis from April 2007 to December 2017 (65 males and 50 females; aged 12–85 years old, median age of 45 years). When counting the number of patients according to the month, from April to September more than 10 patients were treated. Median duration from symptom onset to first visit was 3 days (1–14 days). Eight (7%) of 115 patients had diabetes, and 16 (13.9%) had epiglottic cyst. We divided all the patients into six groups by laryngeal findings according to the classification of Katori and Tsukuda. Number of patients classified as IA, IB, IIA, IIB, IIIA, and IIIB was 41 (35.7%), 21 (18.3%), 22 (19.1%), 15 (13%), 8 (7%), and 8 (7%), respectively. Median duration of hospitalization was 5 days (2–26 days). In the blood test on the first day of hospitalization, the number of white blood cells (WBC) ranged from 3,400 to 25,350/μL (median 10,350/μL) and the C-reactive protein (CRP) ranged from 0.01 to 23.3 mg/dL (median, 2.5 mg/dL). The number of WBC and CRP at the fourth day after the hospitalization was significantly lower than those at the first day. Eight (7%) patients required the airway management such as tracheotomy or cricothyroidotomy. Age, laryngeal finding (severe epiglottis swelling and arytenoid edema; Katori and Tsukuda's classification IIIB), and high inflammatory reaction in blood test (WBC ≥ 20,000/μL and CRP ≥ 20 mg/dL) were the factors that significantly correlated with the airway management.
Functional Effects of the Adams Procedure: A Retrospective Intervention Study
Authors: Kootstra Thomas , van Doesburg Margriet , Schuurman Arnold 
Published: June 2018

Background Injury to the distal radioulnar joint (DRUJ) causes swelling and ulnar-sided wrist pain. The Adams procedure stabilizes the DRUJ and shows promising short-term results.
Purpose We studied the long-term functional outcome in patients who underwent the Adams procedure. We also tested the null hypothesis that there would be no difference in range of motion (ROM) and grip strength between the operated wrist compared to the unaffected side.
Patients and Methods We identified 74 consecutive patients that were operated from March 2005 to February 2014. Twenty-three patients responded to our invitation and underwent clinical follow-up. Three patients had a re-do of the Adams procedure after presenting with postoperative DRUJ instability, one was excluded due to additional wrist surgery not related to the initial procedure. Wrist functionality in the remaining 22 patients was examined by measuring ROM in all planes and grip strength of the operated and non-operated hand. Functional outcome was measured by asking patients to complete the Disabilities of the Arm, Shoulder, and Hand (DASH) outcome measure and the Patient-Rated Wrist and Hand Evaluation (PRWHE).
Results After a mean follow-up time of 5.0 years (standard deviation [SD] 2.0), we found that supination, pronation, and grip strength were significantly decreased in the operated wrist. Postoperative DASH and PRWHE-scores averaged 13.1 (SD 18.6) and 20.3 (SD 15.1), respectively.
Conclusion The Adams procedure affects, but largely restores pronation and supination, and clinical examination, DASH, and PRWHE scores indicate that the Adams procedure leaves patients with upper extremity functionality comparable to a healthy population.
Level of Evidence Level IV.
Passagerer Herzschrittmacher
Authors: Graf Matthias , Stiller Patrick , Karch Martin 
Published: June 2018

AbstractSymptomatic bradycardia is usually caused by abnormalities of atrioventricular conduction or sinus node dysfunction. Reversible and irreversible causes must be considered.Temporary pacemakers are used in the emergency treatment in case of severe bradyarrhythmia.They help to bridge the acute phase until spontaneous restoration of atrioventricular or sinus node function or –if spontaneous restoration fails- until a permanent pacemaker system was implanted.In the following article we discuss the commonly used temporary pacemaker systems. We demonstrate their use and correct programming by an illustrated step by step explanation. For troubleshooting a flow chart was added.
Estimating pseudocounts and fold changes for digital expression measurements
Authors: Erhard Florian 
Published: June 2018

Abstract

Motivation
Fold changes from count based high-throughput experiments such as RNA-seq suffer from a zero-frequency problem. To circumvent division by zero, so-called pseudocounts are added to make all observed counts strictly positive. The magnitude of pseudocounts for digital expression measurements and on which stage of the analysis they are introduced remained an arbitrary choice. Moreover, in the strict sense, fold changes are not quantities that can be computed. Instead, due to the stochasticity involved in the experiments, they must be estimated by statistical inference.

Results
Here, we build on a statistical framework for fold changes, where pseudocounts correspond to the parameters of the prior distribution used for Bayesian inference of the fold change. We show that arbitrary and widely used choices for applying pseudocounts can lead to biased results. As a statistical rigorous alternative, we propose and test an empirical Bayes procedure to choose appropriate pseudocounts. Moreover, we introduce the novel estimator Ψ LFC for fold changes showing favorable properties with small counts and smaller deviations from the truth in simulations and real data compared to existing methods. Our results have direct implications for entities with few reads in sequencing experiments, and indirectly also affect results for entities with many reads.

Availability and implementation
Ψ LFC is available as an R package under https://github.com/erhard-lab/lfc (Apache 2.0 license); R scripts to generate all figures are available at zenodo (doi: 10.5281/zenodo.1163029).

Supplementary information
Supplementary data are available at Bioinformatics online.
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Authors: Kedzierska Katarzyna Z , Gerber Livia , Cagnazzi Daniele , Krützen Michael , Ratan Aakrosh , Kistler Logan 
Published: June 2018

Abstract

Motivation
Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymerase Chain Reaction (PCR) cycle numbers needed for target capture experiments create genotyping noise through polymerase slippage known as PCR stutter.

Results
We developed SONiCS—Stutter mONte Carlo Simulation—a solution for stutter correction based on dense forward simulations of PCR and capture experimental conditions. To test SONiCS, we genotyped a 2499-marker STR panel in 22 humpback dolphins (Sousa sahulensis) using target capture, and generated capillary-based genotypes to validate five of these markers. In these 110 comparisons, SONiCS showed a 99.1% accuracy rate and a 98.2% genotyping success rate, miscalling a single allele in a marker with low sequence coverage and rejecting another as un-callable.

Availability and implementation
Source code and documentation for SONiCS is freely available at https://github.com/kzkedzierska/sonics. Raw read data used in experimental validation of SONiCS have been deposited in the Sequence Read Archive under accession number SRP135756.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nuclear factor E2-related factor 2 deficiency impairs atherosclerotic lesion development but promotes features of plaque instability in hypercholesterolaemic mice
Authors: Ruotsalainen Anna-Kaisa , Lappalainen Jari P , Heiskanen Emmi , Merentie Mari , Sihvola Virve , Näpänkangas Juha , Lottonen-Raikaslehto Line , Kansanen Emilia , Adinolfi Simone , Kaarniranta Kai , Ylä-Herttuala Seppo , Jauhiainen Matti , Pirinen Eija , Levonen Anna-Liisa 
Published: June 2018

Abstract

Aims
Oxidative stress and inflammation play an important role in the progression of atherosclerosis. Transcription factor NF-E2-related factor 2 (Nrf2) has antioxidant and anti-inflammatory effects in the vessel wall, but paradoxically, global loss of Nrf2 in apoE deficient mice alleviates atherosclerosis. In this study, we investigated the effect of global Nrf2 deficiency on early and advanced atherogenesis in alternative models of atherosclerosis, LDL receptor deficient mice (LDLR−/−), and LDLR−/− mice expressing apoB-100 only (LDLR−/− ApoB100/100) having a humanized lipoprotein profile.

Methods and results
LDLR−/− mice were fed a high-fat diet (HFD) for 6 or 12 weeks and LDLR−/−ApoB100/100 mice a regular chow diet for 6 or 12 months. Nrf2 deficiency significantly reduced early and more advanced atherosclerosis assessed by lesion size and coverage in the aorta in both models. Nrf2 deficiency in LDLR−/− mice reduced total plasma cholesterol after 6 weeks of HFD and triglycerides in LDLR−/−ApoB100/100 mice on a chow diet. Nrf2 deficiency aggravated aortic plaque maturation in aged LDLR−/−ApoB100/100 mice as it increased plaque calcification. Moreover, ∼36% of Nrf2−/−LDLR−/−ApoB100/100 females developed spontaneous myocardial infarction (MI) or sudden death at 5 to 12 months of age. Interestingly, Nrf2 deficiency increased plaque instability index, enhanced plaque inflammation and calcification, and reduced fibrous cap thickness in brachiocephalic arteries of LDLR−/−ApoB100/100 female mice at age of 12 months.

Conclusions
Absence of Nrf2 reduced atherosclerotic lesion size in both atherosclerosis models, likely via systemic effects on lipid metabolism. However, Nrf2 deficiency in aged LDLR−/−ApoB100/100 mice led to an enhanced atherosclerotic plaque instability likely via increased plaque inflammation and oxidative stress, which possibly predisposed to MI and sudden death.
Uber, the Taylor Review, Mutuality and the Duty Not to Misrepresent Employment Status
Authors: McGaughey Ewan 
Published: June 2018

Abstract
Do employing entities have a responsibility to not misrepresent the employment status of their staff? This article suggests that recent jurisprudence does create this responsibility. The article starts, first, by discussing the much-awaited Taylor Review, released in July 2017. This purported to address the problems of employment rights and tax in the software-driven ‘gig’ economy. Four main groups of Taylor’s recommendations were to relabel employment statuses and write more secondary legislation, reform tax, cut paid holidays and introduce new ‘soft’ labour rights. These proposals do not address the real issues. Second, this article explains why a test for employment status highlighted by Taylor—‘mutuality of obligation’—has not formed part of binding UK Supreme Court jurisprudence since Autoclenz Ltd v Belcher. Third, it discusses what the Taylor Review did not: the problem of misrepresentation of employment status, which has become closely associated with the gig economy. In October 2017, the Supreme Court issued a path-breaking judgment that changed the requirements for fraud cases, aligning the tests for civil and criminal fraud and therefore making fraud claims easier. This is relevant because of the very serious finding, in Aslam v Uber BV [2017] IRLR 4, [96] by the Employment Tribunal that Uber provided an ‘excellent illustration … of “armies of lawyers” contriving documents in their clients’ interests which simply misrepresent the true rights and obligations on both sides’. This raises the question of whether ‘contriving’ to ‘misrepresent’ something enables fraud claims, either by staff who seek employment rights or by public authorities for tax receipts or social security contributions.