bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep structure of DNA for genomic analysis
Authors: Garzon Max , Mainali Sambriddhi 
Published: September 2021

AbstractRecent advances in next-generation sequencing, deep networks and other bioinformatic tools have enabled us to mine huge amount of genomic information about living organisms in the post-microarray era. However, these tools do not explicitly factor in the role of the underlying DNA biochemistry (particularly, DNA hybridization) essential to life processes. Here, we focus more precisely on the role that DNA hybridization plays in determining properties of biological organisms at the macro-level. We illustrate its role with solutions to challenging problems in human disease. These solutions are made possible by novel structural properties of DNA hybridization landscapes revealed by a metric model of oligonucleotides of a common length that makes them reminiscent of some planets in our solar system, particularly Earth and Saturn. They allow a judicious selection of so-called noncrosshybridizing (nxh) bases that offer substantial reduction of DNA sequences of arbitrary length into a few informative features. The quality assessment of the information extracted by them is high because of their very low Shannon Entropy, i.e. they minimize the degree of uncertainty in hybridization that makes results on standard microarrays irreproducible. For example, SNP classification (pathogenic/non-pathogenic) and pathogen identification can be solved with high sensitivity (~77%/100%) and specificity (~92%/100%, respectively) for combined taxa on a sample of over 264 fully coding sequences in whole bacterial genomes and fungal mitochondrial genomes using machine learning (ML) models. These methods can be applied to several other interesting research questions that could be addressed with similar genomic analyses.
Pulmonary metastasectomy in bone and soft tissue sarcoma with metastasis to the lung
Authors: Gusho Charles A , Seder Christopher W , Lopez-Hisijos Nicolas , Blank Alan T , Batus Marta 
Published: September 2021

Abstract OBJECTIVESThis study investigated the outcomes of sarcoma patients with lung metastases who underwent pulmonary metastasectomy (PM), compared to patients who underwent medical management alone. The secondary objective was to compare survival after PM between variables of interest.METHODSThis was a retrospective review of 565 sarcoma patients with confirmed, isolated pulmonary metastasis identified from the Surveillance, Epidemiology and End Results database between 2010 and 2015. 1:4 propensity score matching was used to select PM and non-PM groups. The multivariable Cox proportional hazards model was used to analyse prognostic factors of disease-free survival (DFS).RESULTSOf the eligible 565 patients, 59 PM patients were matched to 202 non-PM patients in a final ratio of 3.4. After propensity matching, there were no significant differences in baseline characteristics between PM and non-PM patients. The median DFS after PM was 32 months (interquartile range 18–59), compared to 20 months (interquartile range 7–40) in patients without PM (P = 0.032). Using a multivariable Cox proportional hazards model, metastasectomy (hazard ratio 0.536, 95% confidence interval 0.33–0.85; P = 0.008) was associated with improved DFS. In a subset analysis of patients who underwent PM only, the median DFS was longer in males compared to females (P = 0.021), as well as in bone sarcoma compared to soft tissue sarcoma (P = 0.014).CONCLUSIONSFor sarcoma patients with metastatic lung disease, PM appears to improve the prognosis compared to medical management. Furthermore, there may be a survival association with gender and tumour origin in patients who underwent PM. These data may be used to inform the surgical indications and eligibility criteria for metastasectomy in this setting.
Evidence for Human-to-Human Transmission of Hantavirus: A Systematic Review
Authors: Toledo Joao , Haby Michelle M , Reveiz Ludovic , Sosa Leon Leopoldo , Angerami Rodrigo , Aldighieri Sylvain 
Published: September 2021

Abstract

Background
Hantavirus is known to be transmitted from rodents to humans. However, some reports from Argentina and Chile have claimed that the hantavirus strain Andes virus (ANDV) can cause human-to-human transmission of the disease. The aim of this systematic review was to assess the evidence for human-to-human transmission of hantavirus.

Methods
We searched PubMed (inception to 28 February 2021), Cochrane Central, Embase, LILACS and SciELO (inception to 3 July 2020), and other sources. We included studies that assessed whether interpersonal contact with a person with laboratory-confirmed hantavirus infection led to human-to-human transmission. Two reviewers conducted screening, selection, data extraction, and risk of bias assessment.

Results
Twenty-two studies met the inclusion criteria. Meta-analysis was not possible due to heterogeneity. With the exception of 1 prospective cohort study of ANDV in Chile with serious risk of bias, evidence from comparative studies (strongest level of evidence available) does not support human-to-human transmission of hantavirus infection. Noncomparative studies with a critical risk of bias suggest that human-to-human transmission of ANDV may be possible.

Conclusions
The balance of the evidence does not support the claim of human-to-human transmission of ANDV. Well-designed cohort and case-control studies that control for co-exposure to rodents are needed to inform public health recommendations.
Incorporating qualitative research methods into the monitoring and evaluation of neglected tropical disease programmes: a scoping literature review
Authors: Baker Margaret C , Bardosh Kevin , Fitch Elizabeth , Mbabazi Pamela S , Mwingira Upendo , Direny Abdel , Dean Laura , Sutherland Elizabeth G , Krentel Alison 
Published: September 2021

Abstract
This publication addresses the limited use of qualitative methods in neglected tropical disease (NTD) programmes. It describes a scoping literature review conducted to inform the development of a guide to inform the use of rapid qualitative assessments to strengthen NTD mass drug administration (MDA) programmes. The review assessed how qualitative methods are currently used by NTD programmes and identified qualitative approaches from other health and development programmes with the potential to strengthen the design of MDA interventions. Systematic review articles were reviewed and searched using key terms conducted on Google Scholar and PubMed. Results show that methods used by NTD programmes rely heavily on focus group discussions and in-depth interviews, often with time-consuming analysis and limited information on how results are applied. Results from other fields offered insight into a wider range of methods, including participatory approaches, and on how to increase programmatic uptake of findings. Recommendations on how to apply these findings to NTD control are made. The topic of human resources for qualitative investigations is explored and a guide to improve MDAs using qualitative methods is introduced. This guide has direct applicability across the spectrum of NTDs as well as other public health programmes.
High prevalence of HIV-1 transmitted drug resistance and factors associated with time to virological failure and viral suppression in Taiwan
Authors: Huang Szu-Wei , Shen Mei-Chen , Wang Wen-Hung , Li Wei-You , Wang Jen-Hsien , Tseng Cheng-Yin , Liu Po-Yu , Wang Lih-Shinn , Lee Yu-Lin , Chen Yi-Ming Arthur , Lee Chun-Yuan , Lu Po-Liang , Wang Sheng-Fan 
Published: September 2021

AbstractBackgroundIntegrase strand transfer inhibitor (InSTI)-based regimens have become the major first-line treatment for HIV-1-infected patients in Taiwan. Transmitted drug resistance (TDR) and several clinical characteristics are associated with time to virological failure or viral suppression; however, these have not been investigated in Taiwan.ObjectivesTo determine the impact of several factors on treatment outcomes in HIV-1-infected patients in Taiwan.MethodsThe cohort included 164 HIV-1 treatment-naive patients in Taiwan from 2018 to 2020. Blood specimens were collected to determine the genotypic drug resistance using the Stanford University HIV drug resistance database. Cox proportional hazards models were used to identify factors associated with time to virological failure or viral suppression.ResultsThe prevalence of TDR in Taiwan was 27.4% and an increasing trend was seen from 2018 to 2020. TDR mutations related to NNRTIs were the most prevalent (21%) while TDR to InSTIs remained at a relatively low level (1.3%). A baseline HIV-1 viral load of ≥100 000 copies/mL was associated with a shorter time to virological failure [multivariate hazard ratio (mHR) 7.84; P = 0.018] and longer time to viral suppression (mHR 0.46; P &lt; 0.001). Time to viral suppression was shorter in patients receiving InSTI-based regimens (mHR 2.18; P = 0.006). Different InSTI-based regimens as initial treatment did not affect the treatment outcomes.ConclusionsThis study found an increasing trend of HIV-1 TDR prevalence from 2018 to 2020 in Taiwan. Baseline HIV-1 viral load and receiving InSTI-based regimens are important factors associated with time to virological failure or viral suppression.
“Marshall Lecture 2020: The Measure of Monopsony”
Authors: Langella Monica , Manning Alan 
Published: September 2021

Abstract
There has been increasing interest in recent years in monopsony in the labour market. This paper discusses how we can measure monopsony power by combining insights from models based on both frictions and idiosyncrasies. It presents some evidence from the United Kingdom and the United States about how monopsony power varies across the wage distribution within markets, over the business cycle and over time.
Ancient Introgression Between Distantly Related White Oaks (Quercussect.Quercus) Shows Evidence of Climate-Associated Asymmetric Gene Exchange
Authors: O’Donnell Scott T , Fitz-Gibbon Sorel T , Sork Victoria L 
Published: September 2021

AbstractAncient introgression can be an important source of genetic variation that shapes the evolution and diversification of many taxa. Here, we estimate the timing, direction, and extent of gene flow between two distantly related oak species in the same section (Quercus sect. Quercus). We estimated these demographic events using genotyping by sequencing data, which generated 25 702 single nucleotide polymorphisms for 24 individuals of California scrub oak (Quercus berberidifolia) and 23 individuals of Engelmann oak (Quercus engelmannii). We tested several scenarios involving gene flow between these species using the diffusion approximation-based population genetic inference framework and model-testing approach of the Python package DaDi. We found that the most likely demographic scenario includes a bottleneck in Q. engelmannii that coincides with asymmetric gene flow from Q. berberidifolia into Q. engelmannii. Given that the timing of this gene flow coincides with the advent of a Mediterranean-type climate in the California Floristic Province, we propose that changing precipitation patterns and seasonality may have favored the introgression of climate-associated genes from the endemic into the non-endemic California oak.
Cancer Treatment: Preclinical & Clinical
Authors: Abrams Donald I , Velasco Guillermo , Twelves Chris , Ganju Ramesh K , Bar-Sela Gil 
Published: September 2021

Abstract
The first evidence that cannabinoids may have in vitro and in vivo antineoplastic activity against tumor cell lines and animal tumor models was published in the Journal of the National Cancer Institute nearly 50 years ago. Cannabinoids appear to induce apoptosis in rodent brain tumors by way of direct interaction with the cannabinoid receptor. They may inhibit angiogenesis and tumor cell invasiveness. Despite preclinical findings, attempts to translate the benefits from bench to bedside have been limited. This session provides a review of the basic science supporting the use of cannabinoids in gliomas, paired with the first randomized clinical trial of a cannabis-based therapy for glioblastoma multiforme. Another preclinical presentation reports the effects of cannabinoids on triple-negative breast cancer cell lines and how cannabidiol may affect tumors. The session’s second human trial raises concerns about the use of botanical cannabis in patients with advanced cancer receiving immunotherapy suggesting inferior outcomes.
Under Pressure: When Refugees Feel Pressured to Leave Their Host Countries
Authors: Braithwaite Alex , Ghosn Faten , Hameed Tuqa 
Published: September 2021

AbstractA significant portion of the global population of 270 million migrants are refugees who were forcibly displaced from and are unable to return to their country of origin for reasons ranging from personal safety to economic instability. Almost 30 million refugees are protected by an international refugee regime, which obliges host states to provide safehaven and protections against forced expulsion. Nonetheless, refugee experiences in host countries are highly varied, including with respect to how welcome they feel in their host states. This matters because refugees that feel pressured to leave may be more likely to look to move on to a third country or return home involuntarily and before conditions are safe to do so. We argue that whether or not refugees feel pressured to leave host countries is affected by the varied nature of their quotidian interactions with authorities and regular citizens. To test the validity of this argument we draw upon approximately 1,700 responses to a survey administered among the Syrian refugee population throughout Lebanon in June and July 2018. Our statistical analyses demonstrate that individuals who are registered with the UN and the Lebanese government both feel more pressure to leave the country, as do individuals who are subject to ill treatment at the hands of Lebanese residents or authorities. We also find some tentative evidence that individuals who are not well socially connected within Lebanese society—those that live in predominantly Syrian neighbourhoods in Lebanon—also feel more pressure to leave the country.
Cross-validation of the high-capacity tensiometer and thermocouple psychrometer for continuous monitoring of xylem water potential in saplings
Authors: Dainese Roberta , de CFL Lopes Bruna , Tedeschi Giuseppe , Lamarque Laurent J , Delzon Sylvain , Fourcaud Thierry , Tarantino Alessandro 
Published: September 2021

AbstractThe pressure chamber, the most popular method used to measure xylem water potential, is a discontinuous and destructive technique and is therefore not suitable for automated monitoring. Continuous non-destructive monitoring could until very recently be achieved only by use of the thermocouple psychrometer (TP). Here we present the high-capacity tensiometer (HCT) as an alternative method for continuous non-destructive monitoring. This provided us with a unique chance to cross-validate the two instruments by installing them simultaneously on the same sapling stem. The HCT and the TP showed excellent agreement for xylem water potential less than –0.5 MPa. Response to day/night cycles and watering was remarkably in phase, indicating excellent response time of both instruments despite substantially different working principles. For xylem water potential greater than –0.5 MPa, the discrepancies sometimes observed between the HCT and TP were mainly attributed to the kaolin paste used to establish contact between the xylem and the HCT, which becomes hydraulically poorly conductive in this range of water potential once dried beyond its air-entry value and subsequently re-wetted. Notwithstanding this limitation, which can be overcome by selecting a clay paste with higher air-entry value, the HCT has been shown to represent a valid alternative to the TP.
Functional characterization of a cellulose synthase, CtCESA1, from the marine red alga Calliarthron tuberculosum (Corallinales)
Authors: Xue Jan , Purushotham Pallinti , Acheson Justin F , Ho Ruoya , Zimmer Jochen , McFarlane Ciaran , Van Petegem Filip , Martone Patrick T , Samuels A Lacey 
Published: September 2021

Abstract
In land plants and algae, cellulose is important for strengthening cell walls and preventing breakage due to physical forces. Though our understanding of cellulose production by cellulose synthases (CESAs) has seen significant advances for several land plant and bacterial species, functional characterization of this fundamental protein is absent in red algae. Here we identify CESA gene candidates in the calcifying red alga Calliarthron tuberculosum using sequence similarity-based approaches, and elucidate their phylogenetic relationship with other CESAs from diverse taxa. One gene candidate, CtCESA1, was closely related to other putative red algal CESA genes. To test if CtCESA1 encoded a true cellulose synthase, CtCESA1 protein was expressed and purified from insect and yeast expression systems. CtCESA1 showed glucan synthase activity in glucose tracer assays. CtCESA1 activity was relatively low when compared with plant and bacterial CESA activity. In an in vitro assay, a predicted N-terminal starch-binding domain from CtCESA1 bound red algal floridean starch extracts, representing a unique domain in red algal CESAs not present in CESAs from other lineages. When the CtCESA1 gene was introduced into Arabidopsis thaliana cesa mutants, the red algal CtCESA1 partially rescued the growth defects of the primary cell wall cesa6 mutant, but not cesa3 or secondary cell wall cesa7 mutants. A fluorescently tagged CtCESA1 localized to the plasma membrane in the Arabidopsis cesa6 mutant background. This study presents functional evidence validating the sequence annotation of red algal CESAs. The relatively low activity of CtCESA1, partial complementation in Arabidopsis, and presence of unique protein domains suggest that there are probably functional differences between the algal and land plant CESAs.
Of narrative time and space: geography meets history via linguistics
Authors: Franzosi Roberto 
Published: September 2021

Abstract
The article explores issues of narrative time and space. It embraces a conception of geography, of space, as place involving relations among people, with ‘their own stories to tell’. And as story, as narrative, geography can be captured by a ‘story grammar’: Who, What, When, Where, Why, and How (the 5 Ws + H). When and Where, time and space, are the fundamental axes of narrative, different cultures differently grounding narrative in time (the ‘once upon a time’ of Western culture) or in space (the Western Apaches of Arizona). The article explores the ways in which new computational tools allow us to understand and represent actors and their actions in the setting of time and space, ways for geography to meet history, via linguistics. The article illustrates the geographical and historical implications of the approach by focusing on lynching narratives from hundreds of newspaper articles (Georgia, 1875–1930).
On the origin of the Kreutz family of sungrazing comets
Authors: Fernández Julio A , Lemos Pablo , Gallardo Tabaré 
Published: September 2021

ABSTRACT
We evaluate numerically three different models for the parent comet of the Kreutz family of sungrazers: (i) A Centaur on a highly inclined or retrograde orbit that diffuse to the inner planetary region where it became a sungrazer (Model 1). (ii) A parent comet injected from the Oort cloud straight into a near-parabolic, sungrazing orbit. Near perihelion the comet was disrupted by tidal forces from the Sun giving rise to a myriad of fragments that created the Kreutz family (Model 2). (iii) A two-step process by which an Oort cloud comet is first injected in a non-sungrazing, Earth-crossing orbit where its semimajor axis decreases from typical Oort cloud values (a ∼ 104 au) to around 102 au, and then it evolves to a sungrazing orbit by the Lidov–Kozai mechanism (Model 3). Model 1 fails to produce sungrazers of the Kreutz type. Model 2 produces some Kreutz sungrazers and has the appeal of being the most straightforward. Yet the impulses received by the fragments originated in the catastrophic disruption of the parent comet will tend to acquire a wide range of orbital energies or periods (from short-period to long-period orbits) that is in contradiction with the observations. Model 3 seems to be the most promising one since it leads to the generation of some sungrazers of the Kreutz type and, particularly, it reproduces the clustering of the argument of perihelion ω of the observed Kreutz family members around 60°–90°, as a natural consequence of the action of the Lidov–Kozai mechanism.
Properties of Thorne–Żytkow object explosions
Authors: Moriya Takashi J , Blinnikov Sergei I 
Published: September 2021

ABSTRACT
Thorne–Żytkow objects are stars that have a neutron star core with an extended hydrogen-rich envelope. Massive Thorne–Żytkow objects are proposed to explode when the nuclear reactions sustaining their structure are terminated by the exhaustion of the seed elements. In this paper, we investigate the observational properties of the possible Thorne–Żytkow object explosions. We find that Thorne–Żytkow object explosions are observed as long-duration transients lasting for several years. If the accretion disc triggering the explosions does not last for a long time, Thorne–Żytkow object explosions have a luminosity plateau with about $10^{39}\, \mathrm{erg\, s^{-1}}$ lasting for a few years, and then they suddenly become faint. They would be observed as vanished stars after a bright phase lasting for a few years. If the accretion disc is sustained for long time, the Thorne–Żytkow object explosions become as bright as supernovae. They would be observed as supernovae with rise times of several hundred days. We found that their photospheric velocities are $2000\, \mathrm{km\, s^{-1}}$ at most, much smaller than those found in supernovae. Supernovae with extremely long rise times such as HSC16aayt and SN 2008iy may be related to the explosions of Thorne–Żytkow objects.
A method for finding anomalous astronomical light curves and their analogues
Authors: Martínez-Galarza J Rafael , Bianco Federica B , Crake Dennis , Tirumala Kushal , Mahabal Ashish A , Graham Matthew J , Giles Daniel 
Published: September 2021

ABSTRACT
Our understanding of the Universe has profited from deliberate targeted studies of known phenomena, as well as from serendipitous unexpected discoveries, such as the discovery of a complex variability pattern in the direction of KIC 8462852 (Boyajian’s star). Upcoming surveys such as the Vera C. Rubin Observatory Legacy Survey of Space and Time will explore the parameter space of astrophysical transients at all time-scales, and offer the opportunity to discover even more extreme examples of unexpected phenomena. We investigate strategies to identify novel objects and to contextualize them within large time-series data sets in order to facilitate the discovery of new classes of objects as well as the physical interpretation of their anomalous nature. We develop a method that combines tree-based and manifold-learning algorithms for anomaly detection in order to perform two tasks: 1) identify and rank anomalous objects in a time-domain data set; and 2) group those anomalies according to their similarity in order to identify analogues. We achieve the latter by combining an anomaly score from a tree-based method with a dimensionality manifold-learning reduction strategy. Clustering in the reduced space allows for the successful identification of anomalies and analogues. We also assess the impact of pre-processing and feature engineering schemes and investigate the astrophysical nature of the objects that our models identify as anomalous by augmenting the Kepler data with Gaia colour and luminosity information. We find that multiple models, used in combination, are a promising strategy to identify novel light curves and light curve families.