bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nephrectomy improves the survival of metastatic renal cell cancer patients with moderate to good performance status—results from a Finnish nation-wide population-based study from 2005 to 2010
Authors: Laru Lauri , Ronkainen Hanna , Ohtonen Pasi , Vaarala Markku H. 
Published: June 2021

Abstract
Background
The purpose of this study was to evaluate the effects of cytoreductive nephrectomy (CN) and metastasectomies on the survival of patients with synchronous metastatic renal cell cancer (mRCC) using real-life, population-based national dataset.

Methods
Nationwide data, including all cases of synchronous mRCC in Finland diagnosed on a 6-year timeframe, based on the Finnish Cancer Registry and complemented with patient records from the treating hospitals, were analyzed. Patients with Eastern Cooperative Oncology Group (ECOG) performance status 3–4 were excluded. Univariate and adjusted multivariable survival analysis were performed, including subgroup analysis for patients with different medical therapies. Nephrectomy complications were also analyzed.

Results
A total of 732 patients were included in the analysis. CN was performed for 389 (53.1%) patients, whereas 68 (9.3%) patients underwent nephrectomy and metastasectomies of all lesions (surgery with curative intent). Median overall survival (OS) for patients who did not undergo nephrectomy was 5.9 (95% confidence interval [CI] = 4.6–7.2) months. Patients who had a CN had a median OS of 16.6 (95% CI = 14.2–19.1, p < 0.001) months, whereas patients who had surgery with curative intent had a median OS of 51.3 (95% CI = 36.0–66.6, p < 0.001) months. The survival benefit of CN and metastasectomies remained significant in all medical therapy subgroups and in both of the applied multivariable statistical models.

Conclusions
Surgical treatment of metastatic renal cell cancer is associated with a significant survival benefit in patients with good and moderate performance status, regardless of the chosen medical therapy.
Using the longest run subsequence problem within homology-based scaffolding
Authors: Schrinner Sven , Goel Manish , Wulfert Michael , Spohr Philipp , Schneeberger Korbinian , Klau Gunnar W. 
Published: June 2021

AbstractGenome assembly is one of the most important problems in computational genomics. Here, we suggest addressing an issue that arises in homology-based scaffolding, that is, when linking and ordering contigs to obtain larger pseudo-chromosomes by means of a second incomplete assembly of a related species. The idea is to use alignments of binned regions in one contig to find the most homologous contig in the other assembly. We show that ordering the contigs of the other assembly can be expressed by a new string problem, the longest run subsequence problem (LRS). We show that LRS is NP-hard and present reduction rules and two algorithmic approaches that, together, are able to solve large instances of LRS to provable optimality. All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.
Gene expression analysis in EBV-infected ataxia-telangiectasia cell lines by RNA-sequencing reveals protein synthesis defect and immune abnormalities
Authors: Tatfi Moussab , Perthame Emeline , Hillion Kenzo-Hugo , Dillies Marie-Agnès , Menager Hervé , Hermine Olivier , Suarez Felipe 
Published: June 2021

AbstractBackgroundEpstein–Barr virus (EBV) targets B-cells where it establishes a latent infection. EBV can transform B-cells in vitro and is recognized as an oncogenic virus, especially in the setting of immune compromise. Indeed, immunodeficient patients may fail to control chronic EBV infection, leading to the development EBV-driven lymphoid malignancies. Ataxia telangiectasia (AT) is a primary immune deficiency caused by mutations in theATMgene, involved in the repair of double-strand breaks. Patients with AT are at high risk of developing cancers, mostly B-cell lymphoid malignancies, most of which being EBV-related. Aside from immune deficiency secondary to AT, loss of ATM function could also hinder the control of the virus within B-cells, favoring lymphomagenesis in AT patients.ResultsWe used RNA sequencing on lymphoblastoid cell lines derived from patients with AT and healthy donors to analyze and compare both cellular and viral gene expression. We found numerous deregulated signaling pathways involving transcription, translation, oncogenesis and immune regulation. Specifically, the translational defect was confirmed in vitro, suggesting that the pathogenesis of AT may also involve a ribosomal defect. Concomitant analysis of viral gene expression did not reveal significant differential gene expression, however, analysis of EBV interactome suggests that the viral latency genes EBNA-3A, EBNA-3C and LMP1 may be disrupted in LCL from AT patients.ConclusionOur data support the notion that ATM deficiency deregulates cellular gene expression possibly disrupting interactions with EBV latent genes, promoting the oncogenic potential of the virus. These preliminary findings provide a new step towards the understanding of EBV regulation and of AT pathogenesis.
Cancer: a mirrored room between tumor bulk and tumor microenvironment
Authors: Hernández-Camarero Pablo , López-Ruiz Elena , Marchal Juan Antonio , Perán Macarena 
Published: June 2021

AbstractIt has been well documented that the tumor microenvironment (TME) plays a key role in the promotion of drug resistance, the support of tumor progression, invasiveness, metastasis, and even the maintenance of a cancer stem-like phenotype. Here, we reviewed TME formation presenting it as a reflection of a tumor’s own organization during the different stages of tumor development. Interestingly, functionally different groups of stromal cells seem to have specific spatial distributions within the TME that change as the tumor evolves into advanced stage progression which correlates with the fact that cancer stem-like cells (CSCs) are located in the edges of solid tumor masses in advanced tumors.We also focus on the continuos feedback that is established between a tumor and its surroundings. The “talk” between tumor mass cells and TME stromal cells, marks the evolution of both interlocuting cell types. For instance, the metabolic and functional transformations that stromal cells undergo due to tumor corrupting activity.Moreover, the molecular basis of metastatic spread is also approached, making special emphasis on the site-specific pre-metastatic niche formation as another reflection of the primary tumor molecular signature.Finally, several therapeutic approaches targeting primary TME and pre-metastatic niche are suggested. For instance, a systematic analysis of the TME just adjacent to the tumor mass to establish the proportion of myofibroblasts-like cancer-associated fibroblasts (CAFs) which may in turn correspond to stemness and metastases-promotion. Or the implementation of “re-education” therapies consisting of switching tumor-supportive stromal cells into tumor-suppressive ones. In summary, to improve our clinical management of cancer, it is crucial to understand and learn how to manage the close interaction between TME and metastasis.
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion
Authors: Witte Franziska , Ruiz-Orera Jorge , Mattioli Camilla Ciolli , Blachut Susanne , Adami Eleonora , Schulz Jana Felicitas , Schneider-Lunitz Valentin , Hummel Oliver , Patone Giannino , Mücke Michael Benedikt , Šilhavý Jan , Heinig Matthias , Bottolo Leonardo , Sanchis Daniel , Vingron Martin , Chekulaeva Marina , Pravenec Michal , Hubner Norbert , van Heesch Sebastiaan 
Published: June 2021

Abstract
Background
Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines.

Results
We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates.

Conclusions
We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
Controlling bacteriological contamination of environmental surfaces at the biological isolation and containment unit of a veterinary teaching hospital
Authors: Verdial C. , Carneiro C. , Machado I. , Tavares L. , Almeida V. , Oliveira M. , Gil S. 
Published: June 2021

Abstract
Background
The Biological Isolation and Containment Unit (BICU) is a subunit of the Teaching Hospital of the Faculty of Veterinary Medicine of the University of Lisbon, Portugal, for the admission of animals with confirmed infectious diseases or under clinical suspicion and waiting for a diagnosis. As a high-risk environment for the transmission of infectious agents, it is extremely important to implement programs for the surveillance of nosocomial microorganisms in these facilities. The purpose of this study was to evaluate the level of bacterial contamination of the BICU environmental surfaces and to implement corrective actions on disinfection protocols. Swab samples were collected from selected environmental surfaces in 3 different areas of the BICU (isolation, work, and preparatory rooms) to evaluate the total aerobic bacterial load and investigate the presence of 4 nosocomial microorganisms: vancomycin-resistant Enterococcus spp., methicillin-resistant Staphylococcus aureus, 3rd-generation cephalosporin-resistant Escherichia coli, and carbapenem-resistant Pseudomonas aeruginosa. Bacterial quantification was performed by using non-selective media, while specific selective media were used for the isolation of the target microorganisms. Isolates were identified based on their macro and microscopic characteristics and their biochemical profile. Subsequently, new disinfection protocols were implemented, and their effectiveness evaluated.

Results
The surfaces with the highest bacterial load in the isolation, preparatory, and worker’s rooms were the cages, hand-held sponge, and telephone, respectively. Regarding the 4 pathogens investigated, Enterococcus spp. were the most frequently isolated (11.3%), followed by E. coli (1.5%) and P. aeruginosa (1.5%). One of the P. aeruginosa isolates obtained was resistant to imipenem. In the end, new disinfection protocols were implemented, which proved to be effective in reducing bacterial counts by 99.99% in cages and the sponge, and by 90 to 99% on the telephone.

Conclusions
This study allows to conclude that the cages and the human contact surfaces were the most contaminated in the isolation rooms. Nevertheless, the new disinfection strategies seemed to be effective in reducing environmental contamination, including by some potentially nosocomial agents, although more samples must be analyzed for definitive conclusions. These results may contribute to highlight the importance of infection prevention and control measures, as fundamental tools to reduce the spread of infectious agents in the hospital environment.
Estimating Previous Quantization Factors on Multiple JPEG Compressed Images
Authors: Battiato Sebastiano , Giudice Oliver , Guarnera Francesco , Puglisi Giovanni 
Published: June 2021

AbstractThe JPEG compression algorithm has proven to be efficient in saving storage and preserving image quality thus becoming extremely popular. On the other hand, the overall process leaves traces into encoded signals which are typically exploited for forensic purposes: for instance, the compression parameters of the acquisition device (or editing software) could be inferred. To this aim, in this paper a novel technique to estimate “previous” JPEG quantization factors on images compressed multiple times, in the aligned case by analyzing statistical traces hidden on Discrete Cosine Transform (DCT) histograms is exploited. Experimental results on double, triple and quadruple compressed images, demonstrate the effectiveness of the proposed technique while unveiling further interesting insights.
Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin
Authors: Suriano Francesco , Vieira-Silva Sara , Falony Gwen , Roumain Martin , Paquot Adrien , Pelicaen Rudy , Régnier Marion , Delzenne Nathalie M. , Raes Jeroen , Muccioli Giulio G. , Van Hul Matthias , Cani Patrice D. 
Published: June 2021

Abstract
Background
Leptin-deficient ob/ob mice and leptin receptor-deficient db/db mice are commonly used mice models mimicking the conditions of obesity and type 2 diabetes development. However, although ob/ob and db/db mice are similarly gaining weight and developing massive obesity, db/db mice are more diabetic than ob/ob mice. It remains still unclear why targeting the same pathway—leptin signaling—leads to the development of two different phenotypes. Given that gut microbes dialogue with the host via different metabolites (e.g., short-chain fatty acids) but also contribute to the regulation of bile acids metabolism, we investigated whether inflammatory markers, bacterial components, bile acids, short-chain fatty acids, and gut microbes could contribute to explain the specific phenotype discriminating the onset of an obese and/or a diabetic state in ob/ob and db/db mice.

Results
Six-week-old ob/ob and db/db mice were followed for 7 weeks; they had comparable body weight, fat mass, and lean mass gain, confirming their severely obese status. However, as expected, the glucose metabolism and the glucose-induced insulin secretion were significantly different between ob/ob and db/db mice. Strikingly, the fat distribution was different, with db/db mice having more subcutaneous and ob/ob mice having more epididymal fat. In addition, liver steatosis was more pronounced in the ob/ob mice than in db/db mice. We also found very distinct inflammatory profiles between ob/ob and db/db mice, with a more pronounced inflammatory tone in the liver for ob/ob mice as compared to a higher inflammatory tone in the (subcutaneous) adipose tissue for db/db mice. When analyzing the gut microbiota composition, we found that the quantity of 19 microbial taxa was in some way affected by the genotype. Furthermore, we also show that serum LPS concentration, hepatic bile acid content, and cecal short-chain fatty acid profiles were differently affected by the two genotypes.

Conclusion
Taken together, our results elucidate potential mechanisms implicated in the development of an obese or a diabetic state in two genetic models characterized by an altered leptin signaling. We propose that these differences could be linked to specific inflammatory tones, serum LPS concentration, bile acid metabolism, short-chain fatty acid profile, and gut microbiota composition.
Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation
Authors: Ingham Anna Cäcilia , Kielsen Katrine , Mordhorst Hanne , Ifversen Marianne , Aarestrup Frank M. , Müller Klaus Gottlob , Pamp Sünje Johanna 
Published: June 2021

AbstractBackgroundPatients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (aGvHD). It is unknown if, when, and under which conditions a re-establishment of microbial and immunological homeostasis occurs. It is also unclear whether microbiota long-term dynamics occur at other body sites than the gut such as the mouth or nose. Moreover, it is not known whether the patients’ microbiota prior to HSCT holds clues to whether the patient would suffer from severe complications subsequent to HSCT. Here, we take a holobiont perspective and performed an integrated host-microbiota analysis of the gut, oral, and nasal microbiota in 29 children undergoing allo-HSCT.ResultsThe bacterial diversity decreased in the gut, nose, and mouth during the first month and reconstituted again 1–3 months after allo-HSCT. The microbial community composition traversed three phases over 1 year. Distinct taxa discriminated the microbiota temporally at all three body sides, includingEnterococcusspp.,Lactobacillusspp., andBlautiaspp. in the gut. Of note, certain microbial taxa appeared already changed in the patients prior to allo-HSCT as compared with healthy children. Acute GvHD occurring after allo-HSCT could be predicted from the microbiota composition at all three body sites prior to HSCT. The reconstitution of CD4+T cells, TH17, and B cells was associated with distinct taxa of the gut, oral, and nasal microbiota.ConclusionsThis study reveals for the first time bacteria in the mouth and nose that may predict aGvHD. Monitoring of the microbiota at different body sites in HSCT patients and particularly through involvement of samples prior to transplantation may be of prognostic value and could assist in guiding personalized treatment strategies. The identification of distinct bacteria that have a potential to predict post-transplant aGvHD might provide opportunities for an improved preventive clinical management, including a modulation of microbiomes. The host-microbiota associations shared between several body sites might also support an implementation of more feasible oral and nasal swab sampling-based analyses. Altogether, the findings suggest that the microbiota and host factors together could provide actionable information to guiding precision medicine.
Hydrophilization of corn seeds by non-equilibrium gaseous plasma
Authors: Recek Nina , Vesel Alenka , Zaplotnik Rok , Paul Domen , Primc Gregor , Gselman Peter , Mozetič Miran 
Published: June 2021

AbstractPlasma agriculture is a promising niche of interdisciplinary research where the physics, of non-equilibrium gases meets surface chemistry and biological responses. Despite numerous scientific papers, the interaction of gaseous plasma with seeds is not understood enough to make the technique useful in practical agriculture. An obstacle is an improper methodology adopted by different authors. In this paper, we show that the surface wettability does not depend on discharge parameters such as power and pressure, but rather on the fluence of oxygen atoms onto the seed surface. The proper methodology is demonstrated for the case of corn seeds. The surface activation, which enables improved water uptake or good adhesion of a coating, progresses relatively linearly up to the O-atom fluence of 3 × 1024 m−3 and remains constant thereafter. The minimal water contact angle achievable using oxygen plasma treatment is a few degrees.
Two cases of left recurrent laryngeal nerve paralysis after right superior mediastinal node dissection
Authors: Nakamura Yasuyuki , Shindo Yuma , Arai Wataru , Tsuruta Kodai , Maki Ryunosuke , Miyajima Masahiro , Watanabe Atsushi 
Published: June 2021

Abstract
Background
Ipsilateral recurrent laryngeal nerve paralysis is one of the rare complications during the superior mediastinal node dissection for lung cancer. However, very few reports of contralateral recurrent laryngeal nerve paralysis during the procedure are available.

Case presentation
Two women aged 74 and 80 years developed hoarseness after undergoing right upper lobectomy and right superior mediastinal node dissection for primary lung cancer. Postoperative laryngoscopy in the two patients confirmed left vocal cord paralysis.

Conclusion
Node dissection is performed in the standard procedure for right upper lobe lung cancer. At this time, care must be taken not to cause damage not only to the recurrent laryngeal nerve on the ipsilateral side but also to the recurrent laryngeal nerve on the contralateral side.
Sleep Habits of Women With Infertility
Authors: Eisenberg Esther , Legro Richard S , Diamond Michael P , Huang Hao , O’Brien Louise M , Smith Yolanda R , Coutifaris Christos , Hansen Karl R , Santoro Nanette , Zhang Heping 
Published: June 2021

Abstract

Context
Sleep plays important roles in metabolic and reproductive function, and polycystic ovary syndrome (PCOS) is associated with sleep disturbances, including increased prevalence of obstructive sleep apnea.

Objective
We sought to evaluate sleep parameters in infertile women with PCOS compared with women with unexplained infertility (UI) and identify risk factors for disturbed sleep.

Methods
At private and academic ambulatory gynecology and infertility practices, we evaluated a prospective cohort of women diagnosed with PCOS or UI from 2 randomized clinical trials. We included 1603 infertile women enrolled in 2 concurrent randomized clinical trials. The main outcome measures were self-reported sleep measures.

Results
Sleep duration &lt;6 hours (6.1% vs 2.7%; P &lt; .001), habitual snoring (37.8% vs 19.0%; P &lt; .001), and clinical sleepiness (12.0% vs 8.6%; P &lt; .026) were more common in women with PCOS than those with UI. After adjusting for covariates, PCOS and elevated fasting insulin were associated (P = .010) with clinical symptoms of obstructive sleep apnea (OSA) diagnosis, whereas PCOS, elevated insulin (P = .003), WC &gt;88 cm (P = .003), and current smoking (P = .012) were associated with habitual snoring. Clinical depression score (P &lt; .001) and PCOS diagnosis (P = .002) were associated with perceived daytime sleepiness. Short sleep duration and clinical symptoms of OSA were not associated with conception and live birth rates.

Conclusion
Infertile women with PCOS more commonly report sleep disturbances than those with UI. Markers of insulin resistance are associated with previous diagnosis of OSA, habitual snoring, and short sleep duration. The presence of clinical symptoms of OSA or short sleep duration does not affect fertility treatment response.