bluuebunny/crossref_metadata_2025_split huggingface dataset:
The expressed mutational landscape of microsatellite stable colorectal cancers
Authors: Sveen Anita , Johannessen Bjarne , Eilertsen Ina A. , Røsok Bård I. , Gulla Marie , Eide Peter W. , Bruun Jarle , Kryeziu Kushtrim , Meza-Zepeda Leonardo A. , Myklebost Ola , Bjørnbeth Bjørn A. , Skotheim Rolf I. , Nesbakken Arild , Lothe Ragnhild A. 
Published: September 2021

Abstract
Background
Colorectal cancer is the 2nd leading cause of cancer-related deaths with few patients benefiting from biomarker-guided therapy. Mutation expression is essential for accurate interpretation of mutations as biomarkers, but surprisingly, little has been done to analyze somatic cancer mutations on the expression level. We report a large-scale analysis of allele-specific mutation expression.

Methods
Whole-exome and total RNA sequencing was performed on 137 samples from 121 microsatellite stable colorectal cancers, including multiregional samples of primary and metastatic tumors from 4 patients. Data were integrated with allele-specific resolution. Results were validated in an independent set of 241 colon cancers. Therapeutic associations were explored by pharmacogenomic profiling of 15 cell lines or patient-derived organoids.

Results
The median proportion of expressed mutations per tumor was 34%. Cancer-critical mutations had the highest expression frequency (gene-wise mean of 58%), independent of frequent allelic imbalance. Systematic deviation from the general pattern of expression levels according to allelic frequencies was detected, including preferential expression of mutated alleles dependent on the mutation type and target gene. Translational relevance was suggested by correlations of KRAS/NRAS or TP53 mutation expression levels with downstream oncogenic signatures (p < 0.03), overall survival among patients with stage II and III cancer (KRAS/NRAS: hazard ratio 6.1, p = 0.0070), and targeted drug sensitivity. The latter was demonstrated for EGFR and MDM2 inhibition in pre-clinical models.

Conclusions
Only a subset of mutations in microsatellite stable colorectal cancers were expressed, and the “expressed mutation dose” may provide an opportunity for more fine-tuned biomarker interpretations.
Robust Cardinality: a novel approach for cardinality prediction in SQL queries
Authors: B. S. Praciano Francisco D. , Amora Paulo R. P. , Abreu Italo C. , Pereira Francisco L. F. , Machado Javam C. 
Published: September 2021

AbstractBackgroundDatabase Management Systems (DBMSs) use declarative language to execute queries to stored data. The DBMS defines how data will be processed and ultimately retrieved. Therefore, it must choose the best option from the different possibilities based on an estimation process. The optimization process uses estimated cardinalities to make optimization decisions, such as choosing predicate order.MethodsIn this paper, we propose Robust Cardinality, an approach to calculate cardinality estimates of query operations to guide the execution engine of the DBMSs to choose the best possible form or at least avoid the worst one. By using machine learning, instead of the current histogram heuristics, it is possible to improve these estimates; hence, leading to more efficient query execution.ResultsWe perform experimental tests using PostgreSQL, comparing both estimators and a modern technique proposed in the literature. With Robust Cardinality, a lower estimation error of a batch of queries was obtained and PostgreSQL executed these queries more efficiently than when using the default estimator. We observed a 3% reduction in execution time after reducing 4 times the query estimation error.ConclusionsFrom the results, it is possible to conclude that this new approach results in improvements in query processing in DBMSs, especially in the generation of cardinality estimates.
Using bundling to visualize multivariate urban mobility structure patterns in the São Paulo Metropolitan Area
Authors: Martins Tallys G. , Lago Nelson , Santana Eduardo F. Z. , Telea Alexandru , Kon Fabio , de Souza Higor A. 
Published: September 2021

AbstractInternet-based technologies such as IoT, GPS-based systems, and cellular networks enable the collection of geolocated mobility data of millions of people in large metropolitan areas. In addition, large, public datasets are made available on the Internet by open government programs, providing ways for citizens, NGOs, scientists, and public managers to perform a multitude of data analysis with the goal of better understanding the city dynamics to provide means for evidence-based public policymaking. However, it is challenging to visualize huge amounts of data from mobility datasets. Plotting raw trajectories on a map often causes data occlusion, impairing the visual analysis. Displaying the multiple attributes that these trajectories come with is an even larger challenge. One approach to solve this problem is trail bundling, which groups motion trails that are spatially close in a simplified representation. In this paper, we augment a recent bundling technique to support multi-attribute trail datasets for the visual analysis of urban mobility. Our case study is based on the travel survey from the São Paulo Metropolitan Area, which is one of the most intense traffic areas in the world. The results show that bundling helps the identification and analysis of various mobility patterns for different data attributes, such as peak hours, social strata, and transportation modes.
A novel mutation in ACADVL causing very long-chain acyl-coenzyme-A dehydrogenase deficiency in a South Asian pediatric patient: a case report and review of the literature
Authors: Arunath Visvalingam , Liyanarachchi Manoj Sanjeewa , Gajealan Sundararajah , Jasinge Eresha , Weerasekara Kumudu , Moheb Lia Abbasi 
Published: September 2021

Abstract
Background
Very long-chain acyl-coenzyme-A dehydrogenase deficiency is a rare, severe life-threatening metabolic disorder of mitochondrial fatty acid oxidation, caused by mutations in ACADVL gene. Here we present a genetically confirmed case of a South Asian baby girl with severe, early-onset form of very long-chain acyl-coenzyme-A dehydrogenase deficiency due to a novel mutation in ACADVL gene.

Case presentation
Index case was the second baby girl of second-degree consanguineous South Asian parents. She had an uncomplicated antenatal period and was born by spontaneous vaginal delivery at term with a birth weight of 2910 g. She had been noted to have fair skin complexion, hypotonia, and 3 cm firm hepatomegaly. Since birth, the baby developed grunting, poor feeding, and recurrent episodes of symptomatic hypoglycemia and convulsions with multiple semiology. Her septic screening and urine ketone bodies were negative. The baby had high anion gap metabolic acidosis and elevated transaminases and serum creatine phosphokinase levels. Echocardiogram at 4 months revealed bilateral ventricular hypertrophy. Acylcarnitine profile revealed elevated concentrations of tetradecanoylcarnitine (C14), tetradecanoylcarnitine C14:1, and C14:1/C16. Unfortunately, the baby died due to intercurrent respiratory illness at 4 months of age. Sequence analysis of ACADVL gene in perimortem blood sample revealed homozygous frame shift novel variant NM_001270447.1, c.711_712del p.(Phe237Leufs*38), which confirmed the diagnosis of very long-chain acyl-coenzyme-A dehydrogenase deficiency.

Conclusions
This case demonstrates the importance of early diagnosis and management of very long-chain acyl-coenzyme-A dehydrogenase deficiency in improving the outcome of the patients. Implementation of newborn screening using tandem mass spectrometry in Sri Lanka will be beneficial to reduce the morbidity and mortality of treatable disorders of inborn errors.
How effective are lexical richness measures for differentiations of vocabulary proficiency? A comprehensive examination with clustering analysis
Authors: Zhang Yanhui , Wu Weiping 
Published: September 2021

AbstractThis study proposed an innovative automated approach to differentiation of the vocabulary proficiency of Chinese speakers. A robust K-means algorithm was designed to compare the oral proficiency between L1 and L2 Chinese speakers regarding lexical richness and how relatively effective the various lexical measures were in performing the differentiation task. Eighteen lexical richness measures were surveyed and compared using the clustering analysis. The effectiveness of each selected measure as well as an overall evaluation of all the measures for the concerned differentiation tasks were comprehensively calibrated. The results demonstrate that, while the L1 versus L2 group difference in lexical richness was observed with statistical significance for each of the chosen measures, the clustering and membership prediction accuracy of individual speakers varied greatly from one measure to another. The implication is that a more fully defined metric of lexical richness is still a worthwhile endeavor for language proficiency assessment, with optimal directions for such endeavors discussed in the concluding remarks.
Hemorrhagic stroke following snake bite in Burkina Faso (West Africa). A case series
Authors: Dabilgou Alfred Anselme , Sondo Apoline , Dravé Alassane , Diallo Ismael , Kyelem Julie Marie Adeline , Napon Christian , Kaboré Jean 
Published: September 2021

Abstract
Background
Snake bites remain a major medical problem in West Africa, and hemorrhagic stroke following a snakebite has emerged as a rare secondary condition. The objective of this study was to determine the neurological complications following snake bite.

Methods
This study included all the cases of hemorrhagic stroke following snake bite admitted in the neurology Department of Yalgado Ouedraogo University Teaching Hospital during the period from January 1st, 2018 to December 31st 2019.

Results
Three cases of hemorrhagic stroke following snake bite were included in the study. The strokes occurred 4–15 days after the snakebite. Traditional treatment was applied in two cases. Complications were significant, including local manifestations and severe anemia in 2 patients who received blood transfusion. Snake anti-venom was applied. At admission, motor deficit, conscience disorders and fever were the most frequent complaints. Patients received repeated dose of snake anti-venom was applied, antitetanus prophylaxis and antibiotherapy during hospitalization. The majority of the patients had completely recovered.

Conclusions
Hemorrhagic stroke following snake bites are rare in Burkina Faso. Clinical outcome of stroke was favorable after treatment by antivenom, anti-tetanus serum and antibiotics.
Ophiostomatoid fungi associated with pine bark beetles and infested pines in south-eastern Australia, including Graphilbum ipis-grandicollis sp. nov.
Authors: Trollip Conrad , Carnegie Angus J. , Dinh Quang , Kaur Jatinder , Smith David , Mann Ross , Rodoni Brendan , Edwards Jacqueline 
Published: September 2021

AbstractThe ophiostomatoid fungi are an assemblage of ascomycetes which are arguably best-known for their associations with bark and ambrosia beetles (Curculonidae) and blue stain (sap stain) of many economically important tree species. These fungi are considered a significant threat to coniferous forests, which has resulted in numerous studies characterising the diversity of bark beetles and their ophiostomatoid associates globally. The diversity of ophiostomatoid fungi present in Australian pine plantations, however, remains largely undetermined. The aims of this study were therefore to reconsider the diversity of ophiostomatoid fungi associated with Pinus in Australia, and to establish the baseline of expected taxa found within these plantation ecosystems. To achieve this, we reviewed Australian plant pathogen reference collections, and analysed samples collected during forest health surveillance programs from the major pine growing regions in south-eastern Australia. In total, 135 ophiostomatoid isolates (15 from reference collections and 120 collected during the current study) were assessed using morphological identification and ITS screening which putatively distinguished 15 taxonomic groups. Whole genome sequencing (WGS) of representative isolates from each taxon was performed to obtain high-quality sequence data for multi-locus phylogenetic analysis. Our results revealed a greater than expected diversity, expanding the status of ophiostomatoid fungi associated with Pinus in Australia to include 14 species from six genera in the Ophiostomatales and a single species residing in the Microascales. While most of these were already known to science, our study includes seven first records for Australia and the description of one new species, Graphilbum ipis-grandicollis sp. nov.. This study also provides an early example of whole genome sequencing (WGS) approaches replacing traditional PCR-based methods for taxonomic surveys. This not only allowed for robust multi-locus sequence extraction during taxonomic assessment, but also permitted the rapid establishment of a curated genomic database for ophiostomatoid fungi which will continue to aid in the development of improved diagnostic resources and capabilities for Australian biosecurity.
The French Revolution as an Imperial Revolution
Authors: Covo Manuel , Maruschke Megan 
Published: September 2021

AbstractAttempts to reframe the Age of Revolutions as imperial in nature have not fully integrated the French Revolution. Replying to this gap and criticisms of the Revolution's global turn, this essay positions the Revolution as both a moment of imperial reorganization and a sequence of political reinvention that exceed our current categories of empire and nation-state. These arguments open a forum comprising five contributions set in transimperial contexts that span from the Indian to the Atlantic Ocean. The forum offers some points of reflection regarding the narratives, periodizations, and concepts that guide historians of the French Revolution as they navigate the global turn.L'effort historiographique consistant à placer l’ère des révolutions dans leur contexte impérial n'est pas encore parvenu à pleinement intégrer la Révolution française. Cet essai propose de pallier ce manque tout en répondant aux critiques émises à l'encontre du « tournant global ». Il invite à interpréter la Révolution à la fois comme un moment de réorganisation impériale et comme une séquence de réinvention politique, dont le contenu déborde les catégories contemporaines d'empire et d'Etat-nation. Cet essai introduit cinq articles qui analysent la Révolution française dans une variété de contextes transimpériaux, des rives de l'Atlantique à celles de l'océan Indien. Le forum propose quelques points de réflexion critiques sur les récits, les périodisations et les concepts qui informent les modalités d'après lesquelles la Révolution française se voit « mondialisée » par les historiens.
The Directory and the Future of France's Colonial Possessions in Africa, 1795–1802
Authors: Røge Pernille 
Published: September 2021

AbstractThis article examines how French revolutionaries envisioned a republican imperial future in Africa between the decreed abolition of slavery and its restoration under Napoléon. Drawing on proposals within the Ministry of the Marine and the Colonies and analyzing French activities in the Senegambian holdings of Saint-Louis and Gorée, the author argues that, although the French Revolution included numerous creative imperial processes vis-à-vis Africa, they did not amount to an imperial revolution in their own right.Cet article étudie la manière dont les révolutionnaires français envisageaient un avenir impérial et républicain en Afrique entre le décret d'abolition de l'esclavage du 4 février 1794 et sa restauration sous Napoléon. S'appuyant sur des archives manuscrites du ministère de la Marine et des Colonies et analysant les activités françaises à Saint-Louis et Gorée, il démontre que, bien que la Révolution française ait été synonyme de processus impériaux novateurs vis-à-vis de l'Afrique, ces derniers ne constituaient pas pour autant une véritable révolution impériale.
A dai-liao hybrid conjugate gradient method for unconstrained optimization
Authors: Salihu Nasiru , Odekunle Mathew Remilekun , Waziri Mohammed Yusuf , Halilu Abubakar Sani , Salihu Suraj 
Published: September 2021

One of todays’ best-performing CG methods is Dai-Liao (DL) method which depends on non-negative parameter and conjugacy conditions for its computation. Although numerous optimal selections for the parameter were suggested, the best choice of remains a subject of consideration. The pure conjugacy condition adopts an exact line search for numerical experiments and convergence analysis. Though, a practical mathematical experiment implies using an inexact line search to find the step size. To avoid such drawbacks, Dai and Liao substituted the earlier conjugacy condition with an extended conjugacy condition. Therefore, this paper suggests a new hybrid CG that combines the strength of Liu and Storey and Conjugate Descent CG methods by retaining a choice of Dai-Liao parameterthat is optimal. The theoretical analysis indicated that the search direction of the new CG scheme is descent and satisfies sufficient descent condition when the iterates jam under strong Wolfe line search. The algorithm is shown to converge globally using standard assumptions. The numerical experimentation of the scheme demonstrated that the proposed method is robust and promising than some known methods applying the performance profile Dolan and Mor´e on 250 unrestricted problems. Numerical assessment of the tested CG algorithms with sparse signal reconstruction and image restoration in compressive sensing problems, file restoration, image video coding and other applications. The result shows that these CG schemes are comparable and can be applied in different fields such as temperature, fire, seismic sensors, and humidity detectors in forests, using wireless sensor network techniques.
Tibiofemoral contact and alignment in patients with anterior cruciate ligament rupture treated nonoperatively versus reconstruction
Authors: Stockton David J. , Schmidt Andrew M. , Yung Andrew , Desrochers Jane , Zhang Honglin , Masri Bassam A. , Wilson David R. 
Published: September 2021

Aims Anterior cruciate ligament (ACL) rupture commonly leads to post-traumatic osteoarthritis, regardless of surgical reconstruction. This study uses standing MRI to investigate changes in contact area, contact centroid location, and tibiofemoral alignment between ACL-injured knees and healthy controls, to examine the effect of ACL reconstruction on these parameters. Methods An upright, open MRI was used to directly measure tibiofemoral contact area, centroid location, and alignment in 18 individuals with unilateral ACL rupture within the last five years. Eight participants had been treated nonoperatively and ten had ACL reconstruction performed within one year of injury. All participants were high-functioning and had returned to sport or recreational activities. Healthy contralateral knees served as controls. Participants were imaged in a standing posture with knees fully extended. Results Participants’ mean age was 28.4 years (SD 7.3), the mean time since injury was 2.7 years (SD 1.6), and the mean International Knee Documentation Subjective Knee Form score was 84.4 (SD 13.5). ACL injury was associated with a 10% increase (p = 0.001) in contact area, controlling for compartment, sex, posture, age, body mass, and time since injury. ACL injury was associated with a 5.2% more posteriorly translated medial centroid (p = 0.001), equivalent to a 2.6 mm posterior translation on a representative tibia with mean posteroanterior width of 49.4 mm. Relative to the femur, the tibiae of ACL ruptured knees were 2.3 mm more anteriorly translated (p = 0.003) and 2.6° less externally rotated (p = 0.010) than healthy controls. ACL reconstruction was not associated with an improvement in any measure. Conclusion ACL rupture was associated with an increased contact area, posteriorly translated medial centroid, anterior tibial translation, and reduced tibial external rotation in full extension. These changes were present 2.7 years post-injury regardless of ACL reconstruction status. Cite this article: Bone Joint J 2021;103-B(9):1505–1513.
Long-term core outcomes in cauda equina syndrome
Authors: Barker Thomas Patrick , Steele Nick , Swamy Girish , Cook Andrew , Rai Am , Crawford Robert , Lutchman Lennel 
Published: September 2021

Aims Cauda equina syndrome (CES) can be associated with chronic severe lower back pain and long-term autonomic dysfunction. This study assesses the recently defined core outcome set for CES in a cohort of patients using validated questionnaires. Methods Between January 2005 and December 2019, 82 patients underwent surgical decompression for acute CES secondary to massive lumbar disc prolapse at our hospital. After review of their records, patients were included if they presented with the clinical and radiological features of CES, then classified as CES incomplete (CESI) or with painless urinary retention (CESR) in accordance with guidelines published by the British Association of Spinal Surgeons. Patients provided written consent and completed a series of questionnaires. Results In total, 61 of 82 patients returned a completed survey. Their mean age at presentation was 43 years (20 to 77; SD 12.7), and the mean duration of follow-up 58.2 months (11 to 182; SD 45.3). Autonomic dysfunction was frequent: 33% of patients reported bladder dysfunction, and 10% required a urinary catheter. There was a 38% and 53% incidence of bowel and sexual dysfunction, respectively: 47% of patients reported genital numbness. A total of 67% reported significant back pain: 44% required further investigation and 10% further intervention for the management of lower back pain. Quality of life was lower than expected when corrected for age and sex. Half the patients reported moderate or worse depression, and 40% of patients of working age could no longer work due to problems attributable to CES. Urinary and faecal incontinence, catheter use, sexual dysfunction, and genital numbness were significantly more common in patients with CESR. Conclusion This study reports the long-term outcome of patients with CES and is the first to use validated patient-reported outcome measures to assess the CES Core Outcome Set. Persistent severe back pain and on-going autonomic dysfunction were frequently reported at a mean follow-up of five years. Cite this article: Bone Joint J 2021;103-B(9):1464–1471.