bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning approach to extract building footprint from high-resolution images: the case study of Makkah, Saudi Arabia
Authors: Faisal Kamil , Imam Ayman , Majrashi Abdulrahman , Hegazy Ibrahim 
Published: December 2020

Abstract
Extracting and identifying building boundaries from high-resolution images have been a hot topic in the field of remote sensing for years. Various methods including geometric, radiometric, object based and edge detection were previously deliberated and implemented in different studies in the context of building extraction. Nevertheless, the reliability of extraction process is mainly subject to user intervention. The current study proposes a new automatic morphology-based approach for extracting buildings using high-resolution satellite images of Al-Hudaybiyah region in the city of Makkah as a case study. The proposed technique integrates the support vector machine for extracting buildings that have bright and dark roofs. The appropriateness of this method has been examined by means of various indicators for example completeness, correctness and quality. Preliminary findings will illustrate the precision and accuracy of the used machine learning algorithm. Research results can provide a generic indicator to assist the planning authorities in achieving better urban planning processes taking into account all potential environmental, social and urban demands and requirements.
Respiratory Syncytial Virus–Associated Hospitalization Rates among US Infants: A Systematic Review and Meta-Analysis
Authors: McLaughlin John M , Khan Farid , Schmitt Heinz-Josef , Agosti Yasmeen , Jodar Luis , Simões Eric A F , Swerdlow David L 
Published: December 2020

Abstract

Background
Although global reviews of infant respiratory syncytial virus (RSV) burden exist, none have summarized data from the United States or evaluated how RSV burden estimates are influenced by variations in study design.

Methods
We performed a systematic literature review and meta-analysis of studies describing RSV-associated hospitalization rates among US infants and examined the impact of key study characteristics on these estimates.

Results
We reviewed 3328 articles through 14 August 2020 and identified 25 studies with 31 unique estimates of RSV-associated hospitalization rates. Among US infants &lt;1 year of age, annual rates ranged from 8.4 to 40.8 per 1000 with a pooled rate of 19.4 (95% confidence interval [CI], 17.9–20.9). Study type influenced RSV-associated hospitalization rates (P = .003), with active surveillance studies having pooled rates (11.0; 95% CI, 9.8–12.2) that were half that of studies based on administrative claims (21.4; 19.5–23.3) or modeling approaches (23.2; 20.2–26.2).

Conclusions
Applying our pooled rates to the 2020 US birth cohort suggests that 79 850 (95% CI, 73 680–86 020) RSV-associated infant hospitalizations occur each year. The full range of RSV-associated hospitalization rates identified in our review can better inform future evaluations of RSV prevention strategies. More research is needed to better understand differences in estimated RSV burden across study design.
Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis
Authors: Collens Adena B , Katz Laura A 
Published: December 2020

AbstractThrough analyses of diverse microeukaryotes, we have previously argued that eukaryotic genomes are dynamic systems that rely on epigenetic mechanisms to distinguish germline (i.e., DNA to be inherited) from soma (i.e., DNA that undergoes polyploidization, genome rearrangement, etc.), even in the context of a single nucleus. Here, we extend these arguments by including two well-documented observations: (1) eukaryotic genomes interact frequently with mobile genetic elements (MGEs) like viruses and transposable elements (TEs), creating genetic conflict, and (2) epigenetic mechanisms regulate MGEs. Synthesis of these ideas leads to the hypothesis that genetic conflict with MGEs contributed to the evolution of a dynamic eukaryotic genome in the last eukaryotic common ancestor (LECA), and may have contributed to eukaryogenesis (i.e., may have been a driver in the evolution of FECA, the first eukaryotic common ancestor). Sex (i.e., meiosis) may have evolved within the context of the development of germline–soma distinctions in LECA, as this process resets the germline genome by regulating/eliminating somatic (i.e., polyploid, rearranged) genetic material. Our synthesis of these ideas expands on hypotheses of the origin of eukaryotes by integrating the roles of MGEs and epigenetics.
The Combined Effect of Haplodiplonty and Partial Clonality on Genotypic and Genetic Diversity in a Finite Mutating Population
Authors: Stoeckel Solenn , Arnaud-Haond Sophie , Krueger-Hadfield Stacy A 
Published: December 2020

AbstractPartial clonality is known to affect the genetic composition and evolutionary trajectory of diplontic (single, free-living diploid stage) populations. However, many partially clonal eukaryotes exhibit life cycles in which somatic development occurs in both haploid and diploid individuals (haplodiplontic life cycles). Here, we studied how haplodiplontic life cycles and partial clonality structurally constrain, as immutable parameters, the reshuffling of genetic diversity and its dynamics in populations over generations. We assessed the distribution of common population genetic indices at different proportions of haploids, rates of clonality, mutation rates, and sampling efforts. Our results showed that haplodiplontic life cycles alone in finite populations affect effective population sizes and the ranges of distributions of population genetic indices. With nonoverlapping generations, haplodiplonty allowed the evolution of 2 temporal genetic pools that may diverge in sympatry due to genetic drift under full sexuality and clonality. Partial clonality in these life cycles acted as a homogenizing force between those 2 pools. Moreover, the combined effects of proportion of haploids, rate of clonality, and the relative strength of mutation versus genetic drift impacts the distributions of population genetics indices, rendering it difficult to transpose and use knowledge accumulated from diplontic or haplontic species. Finally, we conclude by providing recommendations for sampling and analyzing the population genetics of partially clonal haplodiplontic taxa.
Short-term safety of adjuvant chemoradiotherapy after local resection for patients with high-risk submucosal invasive rectal cancer: a single-arm, multicenter phase II trial
Authors: Noguchi Masaaki , Shitara Kohei , Kawazoe Akihito , Yamamoto Daisuke , Takii Yasumasa , Saito Yutaka , Sato Toshihiko , Horimatsu Takahiro , Ishikawa Hideki , Ito Yoshinori , Ito Masaaki , Ikematsu Hiroaki 
Published: December 2020

Abstract

Background
Surgery is recommended for patients with high-risk submucosal invasive rectal cancer (SM-RC) after local resection but affects the quality of life due to stoma placement or impaired anal function; therefore, alternative treatment approaches are needed to prevent local metastasis. The purpose of this study was to assess the short-term safety of adjuvant chemoradiotherapy with capecitabine in patients with high-risk submucosal invasive rectal cancer after local resection.

Methods
This single-arm, multicenter, phase II trial included patients undergoing local resection for high-risk submucosal invasive rectal cancer within 12 weeks prior to enrollment. High-risk submucosal invasive rectal cancer was defined as the presence of at least one of the following factors: poor differentiation of adenocarcinoma, submucosal invasion depth &gt; 1 mm, presence of lymphovascular invasion and grade-2 or -3 tumour budding. Protocol treatment comprised 45.0 Gy radiotherapy with conventional fractionation and 1650 mg/m2 capecitabine given twice daily until radiotherapy completion. The primary endpoint was treatment completion rate with an expected rate of 95% and a threshold of 80%.

Results
Twenty-nine patients from six institutions were enrolled between May 2015 and February 2018. One patient was ineligible. Twenty-three patients completed treatment, with a completion rate of 82% (80% confidence interval, 69–91%); the remaining five patients completed treatment with protocol deviation. The median relative dose intensity of capecitabine was 100% (range, 58–100%). Common adverse events included radiation dermatitis (54%), anal pain (39%) and anal mucositis (29%). No grade-3 or higher adverse events were reported.

Conclusions
Adjuvant chemoradiotherapy using capecitabine demonstrated acceptable short-term safety profiles in patients with high-risk submucosal invasive rectal cancer after local resection.
The effect of pollen source on seed traits and dispersability in the heterocarpic annualCrepis sancta
Authors: Dener Efrat , Shemesh Hagai , Giladi Itamar 
Published: December 2020

AbstractAimsThe evolution and expression of dispersal-related traits are intertwined with those of other life-history functions and are manifested within various physiological constraints. Such a relationship is predicted between inbreeding levels and dispersability, which may be anatomically and ontogenetically linked so that the selection pressures on one may affect the other. While both the effect of inbreeding on reproductive success and on dispersal strategies received much attention, only a few studies considered both simultaneously. Furthermore, such studies often rely on two dichotomic representations of breeding and dispersal: using selfing versus outcrossing as a representation of breeding level, and dispersal ratio as the sole representation of dispersal strategy.MethodsHere, we used pollination experiments in the heterocarpic Crepis sancta (Asteraceae) to expand in two different manners on the common practice of using dichotomic representations of breeding and dispersal. First, we used pollination treatments that represent a continuum from selfing through pollination by kin to pollination by a distant neighbor. Second, we measured a whole set of continuous morphological and dispersal-related traits, in addition to measurements of reproductive success and dispersal ratio.Important FindingsThe proportion of developed capitula and the number of both dispersed and non-dispersed achenes were significantly lower in the self-pollination treatment in comparison to the outcrossed treatments. The effect of pollen sources on dispersal ratio was not statistically significant, though self-pollinated plants rarely produced non-dispersing seeds. Achene’s biomass increased with distance between parent plants, but pappus width did not, leading to a nonsignificant effect of pollination on falling velocity. Overall, pollen source affected mainly traits that were associated with reproductive output, but it had no clear effect on predominately dispersal-related traits. Such differences in the response of reproduction and dispersal traits to variation in pollen source suggest that dispersal-related selection is probably weak and/or masked by other forces.
Trends in Surgical Volume in the Military Health System—A Potential Threat to Mission Readiness
Authors: Haag Austin , Cone Eugene B , Wun Jolene , Herzog Peter , Lyon Samuel , Nabi Junaid , Marchese Maya , Friedlander David F , Trinh Quoc-Dien 
Published: December 2020

ABSTRACT

Introduction
The Military Health System (MHS) is tasked with a dual mission both to provide medical services for covered patients and to ensure that its active duty medical personnel maintain readiness for deployment. Knowledge, skills, and attitudes (KSA) is a metric evaluating the transferrable skills incorporated into a given surgery or medical procedure that are most relevant for surgeons deployed to a theatre of war. Procedures carrying a high KSA value are those utilizing skills with high relevance for maintaining deployment readiness. Given ongoing concerns regarding surgical volumes at MTFs and the potential adverse impact on military surgeon mission readiness were high-value surgeries to be lost to the civilian sector, we evaluated trends in the setting of high-value surgeries for beneficiaries within the MHS.

Methods
We retrospectively analyzed inpatient admissions data from MTFs and TRICARE claims data from civilian hospitals, 2005-2019, to identify TRICARE-covered patients covered under “purchased care” (referred to civilian facilities) or receiving “direct care” (undergoing treatment at MTFs) and undergoing seven high-value/high-KSA surgeries: colectomy, pancreatectomy, hepatectomy, open carotid endarterectomy, abdominal aortic aneurysm (AAA) repair, esophagectomy, and coronary artery bypass grafting (CABG). Overall and procedure-specific counts were captured, MTFs were categorized into quartiles by volume, and independence between trends was tested with a Cochran–Armitage test, hypothesizing that the proportion of cases referred for purchased care was increasing.

Results
We captured 292,411 cases, including 7,653 pancreatectomies, 4,177 hepatectomies, 3,815 esophagectomies, 112,684 colectomies, 92,161 CABGs, 26,893 AAA repairs, and 45,028 carotid endarterectomies. The majority of cases included were referred for purchased care (90.3%), with the proportion of cases referred increasing over the study period (P &lt; .01). By procedure, all cases except AAA repairs were increasingly referred for treatment over the study period (all P &lt; .01, except esophagectomy P = .04). On examining volume, we found that even the highest-volume-quartile MTFs performed a median of less than one esophagectomy, hepatectomy, or pancreatectomy per month. The only included procedure performed once a month or more at the majority of MTFs was CABG.

Conclusion
On examining volume and referral trends for high-value surgeries within the MHS, we found low surgical volumes at the vast majority of included MTFs and an increasing proportion of cases referred to civilian hospitals over the last 15 years. Our findings illustrate missed opportunities for maintaining the mission readiness of military surgical personnel. Prioritizing the recapture of lost surgical volume may improve the surgical teams’ mission readiness.
Emergency Department Utilization in the U.S. Military Health System
Authors: Dalton Michael K , Andriotti Tomas , Matsas Bridget , Chaudhary Muhammad Ali , Tilley Laura , Lipsitz Stuart , Learn Peter A , Schoenfeld Andrew J , Jarman Molly P , Goralnick Eric 
Published: December 2020

ABSTRACT

Introduction
Emergency department (ED) utilization represents an expensive and growing means of accessing care for a variety of conditions. Prior studies have characterized ED utilization in the general population. We aim to identify the clinical conditions that drive ED utilization in a universally insured population and the impacts of care setting on ED use and admissions in the U.S. Military Health System.

Methods
We queried TRICARE claims data from October 1, 2012, to September 30, 2015, to identify all ED visits for adult patients (age 18-64). The primary presenting diagnoses of all ED visits and those leading to admission are presented with descriptive statistics. Logistic regression was used to identify clinical and sociodemographic factors associated with admission from the ED.

Results
A total of 4,687,205 ED visits were identified, of which 46% took place in the DoD healthcare facilities (direct care). The most common diagnoses across all ED visits were abdominal pain, chest pain, headache, nausea and vomiting, and urinary tract infection. A total of 270,127 (5.8%) ED visits led to inpatient admission. The most common diagnoses leading to admission were chest pain, abdominal pain, depression, conditions relating to acute psychological stress, and pneumonia. For patients presenting with 1 of the 10 most common ED diagnoses, those who were seen at a civilian ED were significantly less likely to be admitted (3.4%) compared to direct care facilities (4.1%) in an adjusted logistic regression model (Adjusted Odds Ratio 0.40 [95% CI: 0.40-0.41], P &lt; .001).

Conclusions
Ultimately, we show that abdominal pain and chest pain are the most common reasons for presentation to the ED in the Military Health System and the most common presenting diagnoses for admission from the ED. Among patients presenting with the most common ED conditions, direct care EDs were significantly more likely to admit patients than civilian facilities.
The 2017 May 20 stellar occultation by the elongated centaur (95626) 2002 GZ32
Authors: Santos-Sanz P , Ortiz J L , Sicardy B , Benedetti-Rossi G , Morales N , Fernández-Valenzuela E , Duffard R , Iglesias-Marzoa R , Lamadrid J L , Maícas N , Pérez L , Gazeas K , Guirado J C , Peris V , Ballesteros F J , Organero F , Ana-Hernández L , Fonseca F , Alvarez-Candal A , Jiménez-Teja Y , Vara-Lubiano M , Braga-Ribas F , Camargo J I B , Desmars J , Assafin M , Vieira-Martins R , Alikakos J , Boutet M , Bretton M , Carbognani A , Charmandaris V , Ciabattari F , Delincak P , Fuambuena Leiva A , González H , Haymes T , Hellmich S , Horbowicz J , Jennings M , Kattentidt B , Kiss Cs , Komžík R , Lecacheux J , Marciniak A , Moindrot S , Mottola S , Pal A , Paschalis N , Pastor S , Perello C , Pribulla T , Ratinaud C , Reyes J A , Sanchez J , Schnabel C , Selva A , Signoret F , Sonbas E , Alí-Lagoa V 
Published: December 2020

ABSTRACT
We predicted a stellar occultation of the bright star Gaia DR1 4332852996360346368 (UCAC4 385-75921) (mV = 14.0 mag) by the centaur 2002 GZ32 for 2017 May 20. Our latest shadow path prediction was favourable to a large region in Europe. Observations were arranged in a broad region inside the nominal shadow path. Series of images were obtained with 29 telescopes throughout Europe and from six of them (five in Spain and one in Greece) we detected the occultation. This is the fourth centaur, besides Chariklo, Chiron, and Bienor, for which a multichord stellar occultation is reported. By means of an elliptical fit to the occultation chords, we obtained the limb of 2002 GZ32 during the occultation, resulting in an ellipse with axes of 305 ± 17 km × 146 ± 8 km. From this limb, thanks to a rotational light curve obtained shortly after the occultation, we derived the geometric albedo of 2002 GZ32 (pV = 0.043 ± 0.007) and a 3D ellipsoidal shape with axes 366 km × 306 km × 120 km. This shape is not fully consistent with a homogeneous body in hydrostatic equilibrium for the known rotation period of 2002 GZ32. The size (albedo) obtained from the occultation is respectively smaller (greater) than that derived from the radiometric technique but compatible within error bars. No rings or debris around 2002 GZ32 were detected from the occultation, but narrow and thin rings cannot be discarded.
Formation of GW190521 from stellar evolution: the impact of the hydrogen-rich envelope, dredge-up, and 12C(α, γ)16O rate on the pair-instability black hole mass gap
Authors: Costa Guglielmo , Bressan Alessandro , Mapelli Michela , Marigo Paola , Iorio Giuliano , Spera Mario 
Published: December 2020

ABSTRACT
Pair-instability (PI) is expected to open a gap in the mass spectrum of black holes (BHs) between ≈40–65 and ≈120 M⊙. The existence of the mass gap is currently being challenged by the detection of GW190521, with a primary component mass of $85^{+21}_{-14}$ M⊙. Here, we investigate the main uncertainties on the PI mass gap: the 12C(α, γ)16O reaction rate and the H-rich envelope collapse. With the standard 12C(α, γ)16O rate, the lower edge of the mass gap can be 70 M⊙ if we allow for the collapse of the residual H-rich envelope at metallicity Z ≤ 0.0003. Adopting the uncertainties given by the starlib database, for models computed with the 12C(α, γ)16O rate $-1\, \sigma$, we find that the PI mass gap ranges between ≈80 and ≈150 M⊙. Stars with MZAMS &gt; 110 M⊙ may experience a deep dredge-up episode during the core helium-burning phase, that extracts matter from the core enriching the envelope. As a consequence of the He-core mass reduction, a star with MZAMS = 160 M⊙ may avoid the PI and produce a BH of 150 M⊙. In the $-2\, {}\sigma {}$ case, the PI mass gap ranges from 92 to 110 M⊙. Finally, in models computed with 12C(α, γ)16O $-3\, {}\sigma {}$, the mass gap is completely removed by the dredge-up effect. The onset of this dredge-up is particularly sensitive to the assumed model for convection and mixing. The combined effect of H-rich envelope collapse and low 12C(α, γ)16O rate can lead to the formation of BHs with masses consistent with the primary component of GW190521.
To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq
Authors: Xu Jinrui , Kudron Michelle M , Victorsen Alec , Gao Jiahao , Ammouri Haneen N , Navarro Fabio C P , Gevirtzman Louis , Waterston Robert H , White Kevin P , Reinke Valerie , Gerstein Mark 
Published: December 2020

AbstractChromatin immunoprecipitation (IP) followed by sequencing (ChIP-seq) is the gold standard to detect transcription-factor (TF) binding sites in the genome. Its success depends on appropriate controls removing systematic biases. The predominantly used controls, i.e. DNA input, correct for uneven sonication, but not for nonspecific interactions of the IP antibody. Another type of controls, ‘mock’ IP, corrects for both of the issues, but is not widely used because it is considered susceptible to technical noise. The tradeoff between the two control types has not been investigated systematically. Therefore, we generated comparable DNA input and mock IP experiments. Because mock IPs contain only nonspecific interactions, the sites predicted from them using DNA input indicate the spurious-site abundance. This abundance is highly correlated with the ‘genomic activity’ (e.g. chromatin openness). In particular, compared to cell lines, complex samples such as whole organisms have more spurious sites—probably because they contain multiple cell types, resulting in more expressed genes and more open chromatin. Consequently, DNA input and mock IP controls performed similarly for cell lines, whereas for complex samples, mock IP substantially reduced the number of spurious sites. However, DNA input is still informative; thus, we developed a simple framework integrating both controls, improving binding site detection.
Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization
Authors: Zhang Wen , Kim Seohyun Chris , Tam Chun Pong , Lelyveld Victor S , Bala Saikat , Chaput John C , Szostak Jack W 
Published: December 2020

Abstract
The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3′-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.