bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Estimation of Deep Atlantic Ventilation from Fossil Radiocarbon Records. I. Modern Reference Estimates
Authors: Marchal Olivier , Zhao Ning 
Published: March 2021

AbstractRadiocarbon dates of fossil carbonates sampled from sediment cores and the seafloor have been used to infer that deep ocean ventilation during the last ice age was different from today. In this first of paired papers, the time-averaged abyssal circulation in the modern Atlantic is estimated by combining a hydrographic climatology, observational estimates of volume transports, Argo float velocities at 1000 m, radiocarbon data, and geostrophic dynamics. Different estimates of modern circulation, obtained from different prior assumptions about the abyssal flow and different errors in the geostrophic balance, are produced for use in a robust interpretation of fossil records in terms of deviations from the present-day flow, which is undertaken in the second paper.For all estimates, the meridional transport integrated zonally and averaged over a hemisphere, 〈Vk〉, is southward between 1000-4000 m in both hemispheres, northward between 4000-5000 m in the South Atlantic, and insignificant between 4000-5000 m in the North Atlantic. Estimates of 〈Vk〉 obtained from two distinct prior circulations - one based on a level of no motion at 4000 m and one based on Argo oat velocities at 1000 m - become statistically indistinguishable when Δ14C data are considered. The transport time scale, defined as τk = /〈Vk〉, where is the volume of the kth layer, is estimated to about a century between 1000-3000 m in both the South and North Atlantic, 124±9 yr (203±23 yr) between 3000-4000 m in the South (North) Atlantic, and 269±115 yr between 4000-5000 m in the South Atlantic.
The Effects of Round Window Membrane Injury and the Use of a Model Electrode Application on Hearing in Rats
Authors: Koc Murat , Dalgic Abdullah , Ozuer Mehmet Ziya 
Published: March 2021

Objective: To investigate the effects of the mechanical trauma to the round window, a model electrode inserted into the scala tympani on the cochlear reserve, and the efficacy of topical steroids in preventing hearing loss. Materials and Methods: 21 male Wistar Albino rats were equally categorized into three groups. In all groups an initial mechanical injury to round window was created. Only subsequent dexamethasone injection was administrated into the cochlea in the subjects of group 2 while a multichannel cochlear implant guide inserted into the cochlea prior to dexamethasone administration for group 3. Distortion product otoacoustic emissions (DPOAEs) were obtained prior to and immediately after the surgical injury, eventually on postoperative seventh day (d 7). Mean signal/noise ratios (S/Ns) obtained at 2000, 3000, and 4000 Hz were calculated. Data sets were compared with non-parametric statistical tests. Results: The early intraoperative mean S/Ns were significantly less than preoperative measurements for group 1 and 2; however, preoperative and postoperative d 7 average S/Ns did not differ. There was statistically significant difference between preoperative, intraoperative and postoperative d 7 average S/Ns for group 3. Conclusion: We observed that hearing was restored approximately to the preoperative levels following early postoperative repair. However, an electrode insertion into the cochlea via round window subsequent to mechanical trauma seems to cause a progressive hearing loss. Therefore, a special care must be taken to avoid the injury to the round window membrane in the course of the placement of a cochlear implant electrode and surgery for the chronic otitis media.
Disease Profile and Oncologic Outcomes After Delayed Diagnosis of Human Papillomavirus–Associated Oropharyngeal Cancer
Authors: Yin Linda X. , Karp Emily E. , Elias Anna , O’Byrne Thomas J. , Routman David M. , Price Daniel L. , Kasperbauer Jan L. , Neben‐Wittich Michelle , Chintakuntlawar Ashish V. , Price Katharine A. , Ma Daniel J. , Foote Robert L. , Moore Eric J. , Van Abel Kathryn M. 
Published: March 2021

ObjectiveDiagnostic delay in human papillomavirus–associated oropharynx squamous cell carcinoma (HPV(+)OPSCC) is common due to nonspecific symptoms. We aim to describe the disease burden and oncologic outcomes of patients with HPV(+)OPSCC diagnosed >12 months after symptom onset.Study DesignThis is a retrospective cohort study of HPV(+)OPSCC patients receiving intent‐to‐cure treatment (including surgery ± adjuvant therapy or primary chemoradiation).Setting2006‐2016, tertiary care center.MethodsTumor stage was compared between patients with and without delayed diagnosis using χ2 tests. Kaplan‐Meier survival analysis with univariate and multivariable Cox regressions were used to determine the effect of diagnostic delay on oncologic outcomes.ResultsIn total, 664 patients were included. Compared to patients diagnosed <12 months from symptom onset (n = 601), those diagnosed at >12 months (n = 63) were more likely to have T4 disease and higher overall American Joint Committee on Cancer (AJCC) clinical stage at presentation (P <. 01 for both). At 5 years, rates of overall survival, cancer‐specific survival, progression‐free survival, and distant metastases–free survival in the delayed diagnosis cohort were 80%, 90%, 80%, and 89%, respectively. A >12‐month delay in diagnosis did not significantly impact overall survival (adjusted hazard ratio [aHR], 1.16; 95% CI, 0.58‐2.31), cancer‐specific survival (aHR, 0.83; 95% CI, 0.29‐2.39), progression‐free survival (aHR, 1.15; 95% CI, 0.56‐2.37), or distant metastases–free survival (aHR, 1.00; 95% CI, 0.42‐2.40) after adjusting for age, sex, and clinical AJCC stage (P >. 05 for all).ConclusionsDelayed diagnosis of HPV(+)OPSCC is associated with greater burden of disease at presentation, but oncologic outcomes remain favorable across treatment modalities. When appropriate, intent‐to‐cure therapy should be pursued despite diagnostic delay.Level of EvidenceLevel III.
Older adults with colon cancer are not different from younger ones, but treated differently: Retrospective analysis from single centre
Authors: Oytun Merve Güner , Bulut Gülcan , Gökmen Erhan , Doğu Burcu B , Karabulut Bülent 
Published: March 2021

Aim Decision- making of the treatment of colon cancer for the older patients becomes more complicated in consequence of comorbidities and geriatric syndromes, most importantly frailty. In the present study, we aimed to investigate whether there is a difference between tumour characteristics, treatment choices, and outcomes between the younger and older adults. Method The patients who were diagnosed with colorectal carcinoma in our centre between 2010 and 2015 included. Clinicopathological features of tumour, treatment choices and survivals of the patients were recorded. Patients were separated into two groups according to their chronological age. Results The present study included 465 patients, there were 173 patients aged 65 years and older. Clinicopathological features were similar in both groups. Adjuvant chemotherapy was given in similar rates. Whereas combination chemotherapies were preferred in younger patients as first-line therapy, single agents were given to the older group(p-value < 0.001). No significant differences were observed between combination therapy and monotherapy as progression-free and overall survival in older adults(p value > 0.05). It was observed that 53.2% of the older patients was not treated with any biological treatment (p-value < 0.001). Discussion Geriatric people are underrepresented in clinical trials,because of the presence of the limitations in the older patients. The results of our study revealed older patients with colon cancer patients underwent surgery less than the younger ones, they recieved monotherapy more frequently as first-line chemotherapy, and less frequently targeted therapy. Their mortality was higher. It was shown that decision-making of colon cancer therapy is influenced by age according to our results.
Leishmania mexicana in a central Texas cat: clinical presentation, molecular identification, sandfly vector collection and novel management
Authors: Hopke Kaitlin , Meyers Alyssa , Auckland Lisa , Hamer Sarah , Florin David , Diesel Alison , Patterson Adam 
Published: March 2021

Case summary This case report documents the clinical appearance, diagnosis and novel treatment of a central Texas cat with cutaneous leishmaniosis. The cat presented with a linear erosion on the right pinnal margin, an ulcerated exophytic nodule on the right hock and a swelling in the right nostril. Cytological and histopathological findings were consistent with leishmaniosis. PCR confirmed the presence of Leishmania mexicana, a species endemic to Texas. An epidemiological investigation was conducted by trapping sandflies from the cat’s environment. Sandflies collected were identified as Lutzomyia species, known vectors of Leishmania species. Given the lack of validated medical therapies for L mexicana in cats, treatments typically prescribed for canine leishmaniosis were administered. Allopurinol achieved clinical success but was discontinued due to suspected drug-related neutropenia. Topical imiquimod also improved lesional skin but was not sustainable due to application difficulty. Oral administration of artemisinin resulted in significant clinical improvement of cutaneous lesions without reported adverse events. Nearly 8 months after the initiation of artemisinin therapy, the cat remained systemically healthy with stable lesions. Relevance and novel information This case report demonstrates endemic feline leishmaniosis in central Texas and provides the clinician with alternative therapeutic options for medical management.
Healthy and Respectful Workplaces: The Experiences of Dental Hygienists in Canada
Authors: Ghoneim A. , Parbhakar K.K. , Farmer J. , Quiñonez C. 
Published: March 2021

Introduction: Like any health care practitioner, dental hygienists can experience mistreatment in the workplace. They can be subjected to harassment, bullying, abuse, and violence. These negative experiences can have adverse consequences on psychological and physical well-being and can lead to job dissatisfaction, depression, and burnout. The aim of this study was to describe dental hygienists’ experiences related to healthy and respectful workplaces. Methods: This was an online self-administered survey sent to all members of the Canadian Dental Hygienists Association. Respondents were asked to report the occurrence, frequency, and impact of different types of mistreatment as experienced over their career. Results: In total, 3,780 dental hygienists responded to the survey (response rate = 22%). More than 70% of respondents experienced some form of mistreatment over their career from dentists, office managers, coworkers, and/or patients. Of those who experienced mistreatment, 67% reported losing the respect they felt for the offending person, 55% reported experiencing symptoms of depression, and 30% quit their job. Conclusions: Mistreatment toward dental hygienists can be prevalent in Canadian dental care settings, resulting in negative consequences to dental hygienists’ well-being. Knowledge Transfer Statement: The findings of this article suggest that measures are needed to support healthy and respectful workplaces in Canadian dental care settings. This includes but is not limited to 1) training and education for all members of the dental care team concerning mistreatment, 2) enacting policies in dental care settings to discourage these types of behaviors, and 3) providing help and support to individuals who experience these incidents.
Homeland as a multi-scalar community: (Dis)continuities in the US security/safety discourse and practice
Authors: Tulumello Simone , Falanga Roberto 
Published: March 2021

This article takes steps from the birth and consolidation of “homeland” as the central discursive engine of the US national security enterprise; and takes issue with the dominant scholarly interpretation of the geographical and spatial implications of its emergence in terms of the dissolution of space and spatialization in security policy ( Bialasiewicz et al., 2007 : 416). We adopt a multi-scalar approach to exploring security discourse/practice, comparing the performativity of national and global security with the local practice/discourse of public safety—with empirical focus on the case of Memphis (TN). Our main arguments are that the homeland builds on the same performative elements of the emergence and consolidation of a certain conception of “community”, as it has become dominant in public safety policymaking at the local scale; and that the homeland/community performativity is the expression of a never-ending movement of production of multi-scalar geographies of the “good” and “evil”, made of the coexistence of centrifugal (pushing problems away) and centripetal (incorporating any given outside) dimensions.
A prognostic score including mutation profile and clinical features for patients with CMML undergoing stem cell transplantation
Authors: Gagelmann Nico , Badbaran Anita , Beelen Dietrich W. , Salit Rachel B. , Stölzel Friedrich , Rautenberg Christina , Becker Heiko , Radujkovic Aleksandar , Panagiota Victoria , Bogdanov Rashit , Christopeit Maximilian , Park Yong , Nibourel Olivier , Luft Thomas , Koldehoff Michael , Corsten Maarten , Heuser Michael , Finke Jürgen , Kobbe Guido , Platzbecker Uwe , Robin Marie , Scott Bart L. , Kröger Nicolaus 
Published: March 2021

Abstract
The inclusion of mutation status improved risk stratification for newly diagnosed patients with chronic myelomonocytic leukemia (CMML). Stem cell transplantation is a potentially curative treatment option, and patient selection is critical because of relevant transplant-related morbidity and mortality. We aimed to evaluate the impact of mutation status together with clinical presentations on posttransplant outcome. Our study included 240 patients with a median follow-up of 5.5 years. A significant association with worse survival was identified for the presence of mutations in ASXL1 and/or NRAS. In multivariable analysis, ASXL1- and/or NRAS-mutated genotype (hazard ratio [HR], 1.63), marrow blasts &gt;2% (HR, 1.70), and increasing comorbidity index (continuous HR, 1.16) were independently associated with worse survival. A prognostic score (CMML transplant score) was developed, and the following points were assigned: 4 points for an ASXL1- and/or NRAS-mutated genotype or blasts &gt;2% and 1 point each for an increase of 1 in the comorbidity index. The CMML transplant score (range, 0-20) was predictive of survival and nonrelapse mortality (P &lt; .001 for both). Up to 5 risk groups were identified, showing 5-year survival of 81% for a score of 0 to 1, 49% for a score of 2 to 4, 43% for a score of 5 to 7, 31% for a score of 8 to 10, and 19% for a score &gt;10. The score retained performance after validation (concordance index, 0.68) and good accuracy after calibration. Predictions were superior compared with existing scores designed for the nontransplant setting, which resulted in significant risk reclassification. This CMML transplant score, which incorporated mutation and clinical information, was prognostic in patients specifically undergoing transplantation and may facilitate personalized counseling.
Immunotherapy perspectives in the new era of B-cell editing
Authors: Ueda Natsuko , Cahen Marine , Danger Yannic , Moreaux Jérôme , Sirac Christophe , Cogné Michel 
Published: March 2021

Abstract
Since the early days of vaccination, targeted immunotherapy has gone through multiple conceptual changes and challenges. It now provides the most efficient and up-to-date strategies for either preventing or treating infections and cancer. Its most recent and successful weapons are autologous T cells carrying chimeric antigen receptors, engineered purposely for binding cancer-specific antigens and therefore used for so-called adoptive immunotherapy. We now face the merger of such achievements in cell therapy: using lymphocytes redirected on purpose to bind specific antigens and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) revolution, which conferred genome-editing methodologies with both safety and efficacy. This unique affiliation will soon and considerably expand the scope of diseases susceptible to adoptive immunotherapy and of immune cells available for being reshaped as therapeutic tools, including B cells. Following the monumental success story of passive immunotherapy with monoclonal antibodies (mAbs), we are thus entering into a new era, where a combination of gene therapy/cell therapy will enable reprogramming of the patient’s immune system and notably endow his B cells with the ability to produce therapeutic mAbs on their own.
Early radical cystectomy with negative margins in a 57-year-old female with myxoid/round cell liposarcoma of the bladder suggests prolonged overall survival
Authors: Delport Johannes Eduard , Makamba Khanyisa 
Published: March 2021

Abstract
Background
Bladder cancer is the 17th most common cancer in the female population. Most bladder cancers are of urothelial origin. Sarcomas of the bladder are very uncommon.

Case presentation
This case concerns a 57-year-old female from a rural town in the Eastern Cape who was diagnosed with myxoid/round cell liposarcoma of the bladder. After the initial transurethral resection of the bladder tumour, she underwent an anterior exenteration with Bricker’s diversion (ileal conduit) and negative margins were achieved.

Conclusions
Sarcomas of the bladder are known to have a poor prognosis. Our patient is alive with good stoma function more than 24 months since her radical surgery. We are of the opinion that her favourable overall survival is attributable to early radical surgical intervention with negative margins.
Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri
Authors: Ducret Valérie , Richards Adam J. , Videlier Mathieu , Scalvenzi Thibault , Moore Karen A. , Paszkiewicz Konrad , Bonneaud Camille , Pollet Nicolas , Herrel Anthony 
Published: March 2021

Abstract
Background
Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes possibly responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach.

Results
We obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization and ATPase activity of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascades. Remarkably, we revealed transcript isoforms of key genes with functions in metabolism, apoptosis, nuclear export and as a transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion.

Conclusion
These results suggest that the differential expression of genes belonging to the pathways of calcium signaling, endoplasmic reticulum stress responses and striated muscle contraction, in addition to the use of alternative splicing and effectors of cellular activity underlie locomotor performance trade-offs. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.
Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T
Authors: Murphy Trevor R. , Xiao Rui , Hamilton-Brehm Scott D. 
Published: March 2021

Abstract
Background
There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface.

Results
The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases.

Conclusions
The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.