bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of long-read methods for sequencing and assembly of a plant genome
Authors: Murigneux Valentine , Rai Subash Kumar , Furtado Agnelo , Bruxner Timothy J C , Tian Wei , Harliwong Ivon , Wei Hanmin , Yang Bicheng , Ye Qianyu , Anderson Ellis , Mao Qing , Drmanac Radoje , Wang Ou , Peters Brock A , Xu Mengyang , Wu Pei , Topp Bruce , Coin Lachlan J M , Henry Robert J 
Published: December 2020

Abstract

Background
Sequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample.

Results
Here, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements.

Conclusions
The 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets
Authors: Johnson Erik C , Wilt Miller , Rodriguez Luis M , Norman-Tenazas Raphael , Rivera Corban , Drenkow Nathan , Kleissas Dean , LaGrow Theodore J , Cowley Hannah P , Downs Joseph , K. Matelsky Jordan , J. Hughes Marisa , P. Reilly Elizabeth , A. Wester Brock , L. Dyer Eva , P. Kording Konrad , R. Gray-Roncal William 
Published: December 2020

Abstract

Background
Emerging neuroimaging datasets (collected with imaging techniques such as electron microscopy, optical microscopy, or X-ray microtomography) describe the location and properties of neurons and their connections at unprecedented scale, promising new ways of understanding the brain. These modern imaging techniques used to interrogate the brain can quickly accumulate gigabytes to petabytes of structural brain imaging data. Unfortunately, many neuroscience laboratories lack the computational resources to work with datasets of this size: computer vision tools are often not portable or scalable, and there is considerable difficulty in reproducing results or extending methods.

Results
We developed an ecosystem of neuroimaging data analysis pipelines that use open-source algorithms to create standardized modules and end-to-end optimized approaches. As exemplars we apply our tools to estimate synapse-level connectomes from electron microscopy data and cell distributions from X-ray microtomography data. To facilitate scientific discovery, we propose a generalized processing framework, which connects and extends existing open-source projects to provide large-scale data storage, reproducible algorithms, and workflow execution engines.

Conclusions
Our accessible methods and pipelines demonstrate that approaches across multiple neuroimaging experiments can be standardized and applied to diverse datasets. The techniques developed are demonstrated on neuroimaging datasets but may be applied to similar problems in other domains.
The Constant Term of Tempered Functions on a Real Spherical Space
Authors: Delorme Patrick , Krötz Bernhard , Souaifi Sofiane , Beuzart-Plessis Raphaël 
Published: December 2020

Abstract
Let $Z$ be a unimodular real spherical space. We develop a theory of constant terms for tempered functions on $Z$, which parallels the work of Harish-Chandra. The constant terms $f_I$ of an eigenfunction $f$ are parametrized by subsets $I$ of the set $S$ of spherical roots that determine the fine geometry of $Z$ at infinity. Constant terms are transitive i.e., $(f_J)_I=f_I$ for $I\subset J$, and our main result is a quantitative bound of the difference $f-f_I$, which is uniform in the parameter of the eigenfunction.
SARS-CoV-2 Serologic Immune Response in Exogenously Immunosuppressed Patients
Authors: Zilla Megan L , Keetch Christian , Mitchell Gretchen , McBreen Jeffery , Shurin Michael R , Wheeler Sarah E 
Published: December 2020

Abstract

Background
While it is presumed that immunosuppressed patients, such as solid organ transplant recipients on immunosuppression, are at greater risk from SARS-CoV-2 infection than the general population, the antibody response to infection in this patient population has not been studied.

Methods
In this report, we follow the anti-SARS-CoV-2 antibody levels in patients with COVID-19 who are undergoing exogenous immunosuppression. Specifically, we studied the antibody response of 3 solid organ transplant recipient patients, 3 patients who take daily inhaled fluticasone, and a patient on etanercept and daily inhaled fluticasone, and compared them to 5 patients not on exogenous immunosuppression.

Results
We found that the solid organ transplant patients on full immunosuppression are at risk of having a delayed antibody response and poor outcome. We did not find evidence that inhaled steroids or etanercept predispose patients to delayed immune response to SARS-CoV-2.

Conclusion
The data presented here suggest that solid organ transplant recipients may be good candidates for early targeted intervention against SARS-CoV-2.
The hip asphericity angle: a novel angle for measurement of Cam-FAI correction
Authors: Masoud Mohammad , Apivatgaroon Adinun , Said Hatem , Abdel-Hamid Mohamed M , El-Assal Maher , Dienst Michael 
Published: December 2020

Abstract
The alpha angle is routinely used for the diagnosis and quantitative description of the Cam deformity of the hip. However, a reliable identification of the femoral neck axis as its reference line can be difficult. Moreover, most cam resections include a reduction of the femoral neck diameter with an automatic posteromedial angulation of the femoral neck axis. In consequence, the reference axes for the pre- and postoperative alpha angles are different, and a comparison of both angles underlies a systematic error to relatively higher postoperative alpha angles. In order to avoid this systemic error, we propose the hip asphericity (HA) angle with a reference axis independent of the amount of bony resection. Two retrospective groups were formed, a ‘femoroacetabular impingement (FAI) group’ that had hip arthroscopy for cam resection and a ‘Control group’ without cam deformity. The alpha and HA angles were measured by three examiners. The measurements were repeated 1 month later. In the FAI group, offset correction was calculated using both angles. Statistically significant differences for both the alpha and the HA angles were found between the control and the preoperative FAI group as well as between the preoperative and postoperative FAI groups. The HA angle-correction by a mean of 27.5° was significantly higher in comparison to the alpha angle correction by a mean of 25.4°. The intertester and intratester reliability of both angles were not significantly different. The HA angle is a new and reliable radiographic parameter for measuring cam deformity and proves superior in measuring cam correction.
Treatment of type IV Pipkin fracture in patients with a high BMI via hip arthroscopy-assisted surgery: a case report
Authors: Hsu Shan-Ling , Chen Chung-Yang , Hsu Chi-Hsiang 
Published: December 2020

Abstract
Pipkin type IV femoral head (FH) fracture–dislocations are usually treated via open surgery. There are many surgical approaches for the treatment of this difficult fracture depending on the fracture pattern. Obesity presents another challenging problem in surgical treatment and sometimes leads to a poorer outcome. We discuss herein a patient of a high body mass index (BMI) with a Pipkin type IV FH fracture who underwent open reduction internal fixation (ORIF) of anacetabular fracture with reconstruction plates and hip arthroscopy-assisted fixation of the FH fracture with two Herbert screws via the posterior approach. The intra-articular osteochondral loose bodies were excised by hip arthroscopy simultaneously. The joint congruency and screw positions were checked during surgery by arthroscopy. After 6 months, clinical and computed tomography (CT) follow-ups showed excellent results. The patient of a high BMI recovered immediately and had a satisfactory short-term outcome after hip arthroscopy-assisted surgery. We concluded that hip arthroscopy-assisted surgery is a viable option for the treatment of Pipkin type IV FH fracture–dislocations.
Deep Learning Image Analysis of Benign Breast Disease to Identify Subsequent Risk of Breast Cancer
Authors: Vellal Adithya D , Sirinukunwattan Korsuk , Kensler Kevin H , Baker Gabrielle M , Stancu Andreea L , Pyle Michael E , Collins Laura C , Schnitt Stuart J , Connolly James L , Veta Mitko , Eliassen A Heather , Tamimi Rulla M , Heng Yujing J 
Published: December 2020

Abstract

Background
New biomarkers of risk may improve breast cancer (BC) risk prediction. We developed a computational pathology method to segment benign breast disease (BBD) whole slide images into epithelium, fibrous stroma, and fat. We applied our method to the BBD BC nested case-control study within the Nurses’ Health Studies to assess whether computer-derived tissue composition or a morphometric signature was associated with subsequent risk of BC.

Methods
Tissue segmentation and nuclei detection deep-learning networks were established and applied to 3795 whole slide images from 293 cases who developed BC and 1132 controls who did not. Percentages of each tissue region were calculated, and 615 morphometric features were extracted. Elastic net regression was used to create a BC morphometric signature. Associations between BC risk factors and age-adjusted tissue composition among controls were assessed using analysis of covariance. Unconditional logistic regression, adjusting for the matching factors, BBD histological subtypes, parity, menopausal status, and body mass index evaluated the relationship between tissue composition and BC risk. All statistical tests were 2-sided.

Results
Among controls, direction of associations between BBD subtypes, parity, and number of births with breast composition varied by tissue region; select regions were associated with childhood body size, body mass index, age of menarche, and menopausal status (all P &lt; .05). A higher proportion of epithelial tissue was associated with increased BC risk (odds ratio = 1.39, 95% confidence interval = 0.91 to 2.14, for highest vs lowest quartiles, Ptrend = .047). No morphometric signature was associated with BC.

Conclusions
The amount of epithelial tissue may be incorporated into risk assessment models to improve BC risk prediction.
Surgery with the Motec total wrist replacement: learning from earlier designs
Authors: Clough Oliver T , Lee George , Hayter Edward , Hardman John , Anakwe Raymond E 
Published: December 2020

Abstract
The design of and applications for wrist arthroplasty continue to evolve but lag behind the results for hip and knee arthroplasty with respect to demonstrable durability and effectiveness. As we develop our knowledge, experience and the indications for wrist replacement surgery, it is important that we learn from past design and surgical experience. We report the case of a female patient treated with a Motec cementless metal-on-metal wrist replacement (Swemac Orthopaedics AB, Linköping, Sweden) for post-traumatic arthritis of the radiocarpal joint. Based on our experience with this case and others, we make two specific technical recommendations to improve the success and longevity of this implant.
Metastatic renal cell carcinoma presenting as jaundice with biliary and gastric outlet obstruction. A case report
Authors: Iqbal Ramiz , Wiadji Elvina 
Published: December 2020

Abstract
Renal cell carcinoma (RCC) can be an aggressive malignancy that has a propensity to spread to atypical locations, most commonly to lung, bone, lymph node. RCC presenting as obstructive jaundice with gastric outlet obstruction has rarely been cited in literature. This study presents a case of advanced RCC in a patient with obstructive jaundice and associated gastric outlet obstruction from a large right renal RCC with malignant retrocaval lymphadenopathy invading the duodenum and distal common bile duct. The patient underwent anterograde stenting of the biliary system via a percutaneous transhepatic cholangiography and an insertion of a duodenal stent. Immunotherapy was commenced and the patient was discharged home. This case highlights the importance of a multi-disciplinary team approach to the management of a complex surgical patient.
Retrocaval ureter: a case report
Authors: Al-Hajjaj Maher , Tallaa Mohamed 
Published: December 2020

Abstract
Retrocaval ureter or circumcaval ureter is considered a rare congenital anomaly. We reported a case of 48-year-old woman who presented with right flank pain. In investigations, we found a retreocaval ureter that was treated surgically. In conclusion, retrocaval ureter is rare cause of flank pain and one of the challenging cases for urologists that needs careful investigations.
Immunoglobulin A nephropathy in association with inflammatory bowel diseases: results from a national study and systematic literature review
Authors: Joher Nizar , Gosset Clément , Guerrot Dominique , Pillebout Evangeline , Hummel Aurélie , Boffa Jean-Jacques , Faguer Stanislas , Rabant Marion , Higgins Sarah , Moktefi Anissa , Delmas Yahsou , Karras Alexandre , Lapidus Nathanaël , Amiot Aurélien , Audard Vincent , El Karoui Khalil 
Published: December 2020

Abstract

Background
Little is known about clinical characteristics and kidney outcomes in patients with biopsy-proven immunoglobulin A nephropathy (IgAN) in a context of inflammatory bowel disease (IBD).

Methods
We conducted a retrospective multicentre study with a centralized histological review to analyse the presentation, therapeutic management and outcome of 24 patients suffering from IBD-associated IgAN relative to a cohort of 134 patients with primary IgAN without IBD.

Results
Crohn’s disease and ulcerative colitis accounted for 75 and 25% of IBD-associated IgAN cases, respectively. IBD was diagnosed before IgAN in 23 cases (a mean of 9 years previously) and was considered active at IgAN onset in 23.6% of patients. Hypertension was present in 41.7% of patients. The urinary protein:creatinine ratio exceeded 100 mg/mmol in 70.8% of patients (mean 254 mg/mmol). Estimated glomerular filtration rate (eGFR) was &gt;60 mL/min/1.73 m2 in 13/24 patients and only 1 patient required dialysis. In the Oxford mesangial hypercellularity, endocapillary cellularity, segmental sclerosis and interstitial fibrosis/tubular atrophy with crescents classification of renal biopsies, 57% were M1, 48% E1, 76% S1, 57% T1–2 and 38% C1–2. Steroids were administered in 50% of cases. After a mean follow-up of 7.2 years, 4 patients (16.7%) had a poor kidney outcome: end-stage renal disease (n = 3) or a &gt;50% decrease in eGFR from initial values (n = 1). A similar evolution was observed in patients with primitive IgAN.

Conclusions
This first case series suggests that IBD-associated IgAN has frequent inflammatory lesions at onset and variable long-term outcomes.
Effect of dietary carbohydrate and lipid modification on clinical and anthropometric parameters in nonalcoholic fatty liver disease: a systematic review and meta-analysis
Authors: Garcêz Lais S , Avelar Camila R , Fonseca Nedja S S , Costa Priscila R F , Lyra André C , Cunha Carla M , Jesus Rosangela P , Oliveira Lucivalda P M 
Published: December 2020

Abstract

Context
Nonalcoholic fatty liver disease (NAFLD) is estimated to affect approximately 25% of the adult population, making it one of the most common chronic liver diseases worldwide and a major public health problem. Still, there is no consensus on the most appropriate nutritional intervention for disease treatment.

Objective
To systematize and synthesize the results of randomized controlled trials that have evaluated the effect of dietary interventions with different, quantitative, macronutrient compositions on hepatic steatosis attenuation, serum levels of alanine aminotransferase, aspartate aminotransferase, lipid profile, glucose metabolism markers, and anthropometric parameters of adults and the elderly (age ≥ 60 years) with NAFLD.

Data Sources
MEDLINE databases via PubMed, Embase, Science Direct, LILACS, Web of Science, ClinicalTrials.gov, and Cochrane Library were searched. Randomized controlled trials that compared interventions as diets with values ≤ 45% or 20% of the total daily energy intake from carbohydrates or lipids, respectively, compared with dietary reference intakes, were included.

Data Extraction
Risk of bias was assessed through the Cochrane Collaboration tool. The meta-analysis was only performed to evaluate the effect of carbohydrate-modified diets on the outcome variables. The number of participants and mean values and respective standard deviations of the outcome variables were extracted and used to calculate weighted mean differences and their respective 95%CIs.

Results
The search strategy resulted in 21 146 studies, of which 10 were retained for qualitative analysis and 6 were included in the meta-analysis. From the analysis of 10 studies were identified 8 articles in which low-calorie diets were evaluated and 3 interventions that used an isocaloric diet. Only 3 studies were classified as having low risk of bias.

Conclusion
The observed effects on hepatic steatosis, serum alanine aminotransferase and aspartate aminotransferase levels, parameters of lipid and glucose metabolism, and anthropometric variables were mostly related to a hypocaloric diet. The use of reduced macronutrient interventions had no efficacy.

Systematic Review Registration
PROSPERO registration no. CRD42018088824.
The Long-Term Relationship Between Psychological Resilience, Psychosis, Distress, and Suicidal Thoughts and Behaviors
Authors: Harris Kamelia , Haddock Gillian , Peters Sarah , Gooding Patricia 
Published: December 2020

AbstractSuicide deaths in people with non-affective psychosis represent a major health care concern. Previous research has shown that psychosis and the associated distress increase suicidal experiences, whereas psychological resilience weakens the impact of suicide precursors, such as defeat, entrapment, and hopelessness on suicidal experiences. The moderating roles of psychosis, distress, and psychological resilience in the relationships between defeat, entrapment, hopelessness, and suicidal thoughts and behaviors have not been tested longitudinally. This 3-month longitudinal study used moderated mediation analysis to investigate: (1) the impact of defeat/entrapment and hopelessness on suicidal thoughts and behaviors and (2) the moderating effects of psychosis, distress, and psychological resilience in the relationships between defeat/entrapment, hopelessness, and suicidal thoughts and behaviors. Individuals with non-affective psychosis-related diagnosis (including schizophrenia, schizophreniform disorder, schizoaffective disorder, delusional disorder, or psychotic disorders not otherwise specified) and lifetime experiences of suicidal thoughts, plans, and/or acts were recruited from the North-West of England, UK. Of the 100 participants at baseline, 90 took part in the follow-up assessment. At baseline, most of the participants had experienced one or more lifetime suicide attempts. Suicidal thoughts and behaviors scores were significantly lower at follow-up, compared with baseline. Over time, defeat/entrapment predicted suicidal thoughts and behaviors when the severity of psychosis and the associated distress were moderate and high, and resilience was lowest. The impact of defeat/entrapment, psychosis, distress due to psychosis, and resilience needs to be incorporated into interventions aiming to reduce suicidal experiences. These findings impact psychosis and resilience-focused suicide prevention interventions for people with non-affective psychosis.
A new method for detecting solar atmospheric gravity waves
Authors: Calchetti Daniele , Jefferies Stuart M. , Fleck Bernhard , Berrilli Francesco , Shcherbik Dmitriy V. 
Published: December 2020

Internal gravity waves have been observed in the Earth’s atmosphere and oceans, on Mars and Jupiter, and in the Sun’s atmosphere. Despite ample evidence for the existence of propagating gravity waves in the Sun’s atmosphere, we still do not have a full understanding of their characteristics and overall role for the dynamics and energetics of the solar atmosphere. Here, we present a new approach to study the propagation of gravity waves in the solar atmosphere. It is based on calculating the three-dimensional cross-correlation function between the vertical velocities measured at different heights. We apply this new method to a time series of co-spatial and co-temporal Doppler images obtained by SOHO/MDI and Hinode/SOT as well as to simulations of upward propagating gravity wave-packets. We show some preliminary results and outline future developments.
This article is part of the Theo Murphy meeting issue ‘High-resolution wave dynamics in the lower solar atmosphere’.
The dynamics of 3-min wavefronts and their relation to sunspot magnetic fields
Authors: Sych Robert , Jess David B. , Su Jiangtao 
Published: December 2020

We present a study of wave processes occurring in solar active region NOAA 11131 on 10 December 2010, captured by the Solar Dynamics Observatory in the 1600 Å, 304 Å and 171 Å channels. For spectral analysis, we employed pixelized wavelet filtering together with a developed digital technique based on empirical mode decomposition. We studied the ∼3-minute wave dynamics to obtain relationships with the magnetic structuring of the underlying sunspot. We found that during development of wave trains the motion path occurred along a preferential direction, and that the broadband wavefronts can be represented as a set of separate narrowband oscillation sources. These sources become visible as the waves pass through the umbral inhomogeneities caused by the differing magnetic field inclination angles. We found the spatial and frequency fragmentation of wavefronts, and deduced that the combination of narrowband spherical and linear parts of the wavefronts provide the observed spirality. Maps of the magnetic field inclination angles confirm this assumption. We detect the activation of umbral structures as the increasing of oscillations in the sources along the front ridge. Their temporal dynamics are associated with the occurrence of umbral flashes. Spatial localization of the sources is stable over time and depends on the oscillation period. We propose that these sources are the result of wave paths along the loops extending outwards from the magnetic bundles of the umbra.
This article is part of the Theo Murphy meeting issue ‘High-resolution wave dynamics in the lower solar atmosphere’.