bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-distance dispersal events rather than growth habit and life-history traits affect diversification rate in tribe Apieae (Apiaceae)
Authors: Frankiewicz Kamil E , Banasiak Łukasz , Oskolski Alexei , Reduron Jean-Pierre , Reyes-Betancort Jorge Alfredo , Alsarraf Mohammed , Trzeciak Paulina , Spalik Krzysztof 
Published: April 2021

AbstractFactors influencing diversification rates may be of intrinsic (e.g. morphological novelties) or extrinsic (e.g. long-distance dispersal, availability of ecological niches) nature. Growth habit may influence diversification rates because herbaceous plants often have shorter generation times and a more pronounced r reproductive strategy than their woody relatives. We examined life history and habit evolution, wood anatomy and biogeographical history of Apiaceae tribe Apieae in conjunction with diversification rate analysis to explore which factors may have affected clade species richness and to elucidate the constraints on the evolution of secondary woodiness in this group. We demonstrate that diversification rates are similar in morphologically homogeneous and diverse clades and in herbaceous and woody lineages. The only clade with a significantly elevated diversification rate is Southern Hemisphere Apium, in which diversity probably resulted from several long-distance dispersal events. We also show that wood anatomy in herbaceous and woody species does not differ considerably regardless of their continental or insular origin, but it is affected by stem architecture and plant reproductive strategy. As the taxonomy of Apieae suffers from inflation with numerous monotypic genera, we propose to include Canaria in Rutheopsis, and Foeniculum, Schoenoselinum, Ridolfia and Pseudoridolfia in Anethum.
Micro-MRI improves the accuracy of clinical diagnosis in cerebral small vessel disease
Authors: Ishikawa Hidehiro , Niwa Atsushi , Kato Shinya , Ii Yuichiro , Shindo Akihiro , Matsuura Keita , Nishiguchi Yamato , Tamura Asako , Taniguchi Akira , Maeda Masayuki , Hashizume Yoshio , Tomimoto Hidekazu 
Published: April 2021

Abstract
Even with postmortem pathological examination, only limited information is provided of the foci of in vivo clinical information. Cerebral small vessel disease, which is associated with ageing, dementia and stroke, highlights the difficulty in arriving at a definitive diagnosis of the lesions detected on in vivo radiological examination. We performed a radiological−pathological comparative study using ex vivo MRI to examine small cerebral lesions. Four patients with small vessel disease lesions detected on in vivo MRI were studied. Exact pathological findings of in vivo MRI-detected lesions were revealed. The ischaemic lesion after 17 days from onset showed positivity for peroxiredoxin, cluster of differentiation 204 and glial fibrillary acidic protein, indicating sterile inflammation and neuroprotective reaction. Cortical microinfarcts beneath the cortical superficial siderosis were associated with inflammation from the superficial layer in a patient with cerebral amyloid angiopathy; in this patient, a bilinear track-like appearance of the cortical superficial siderosis on the ex vivo MRI was compatible with iron deposition on the pia matter and within cortical layers II–III. An in vivo MRI-detected cerebral microbleed was revealed to be heterogeneous. An in vivo MRI-detected cerebral microbleed was revealed to be a venous angioma. Furthermore, a neuropathologically confirmed embolic cerebral microbleed was firstly detected using this method. Our results suggest that in vivo MRI-detected lobar cerebral microbleeds can be caused by non-cerebral amyloid angiopathy aetiologies, such as microembolism and venous angioma. Venous angioma and embolic microbleeds may mimic cerebral amyloid angiopathy markers on in vivo MRI. To clarify the clinical importance of these lesions, we should investigate their rate and frequency in a large cohort of healthy individuals and patients with cardiac risk factors. Thus, we provide evidence that ex vivo micro-MRI improves the clinical diagnosis of small vessel diseases.
Determination of Organophosphorus Pesticides Using Solid-Phase Extraction Followed by Gas Chromatography–Mass Spectrometry
Authors: Sun Peng , Zheng Shusheng , Yan Rui , Lian Yongfu 
Published: April 2021

Abstract
In this study, a method was developed for determination of three organophosphorus pesticides (OPPs) using graphene aerogel solid-phase extraction (SPE) combined with gas chromatography–mass spectrometry (GC–MS). The experimental results showed that the target analytes could be extracted on packed SPE cartridges and then eluted with tetrahydrofuran. The final sample solution was analyzed by GC–MS, which demonstrated good linearity between 0.5 and 500 μg L−1 with a correlation coefficient (r) of 0.9991–0.9998. The limits of detection (S/N = 3) and the limits of quantification (S/N = 10) for the three OPPs ranged from 0.38 to 0.82 μg L−1 and 1.32 to 2.75 μg L−1, respectively. The accuracy of the proposed method was evaluated by measuring the recovery of the spiked samples, which ranged from 91.2 to 103.7%, with relative standard deviations of 2.1–7.2%. This method was successfully applied for the determination of the target analytes in water samples taken from tap, wetlands and canal water.
Ultra-sensitive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antigen Detection for the Diagnosis of Coronavirus Disease 2019 (COVID-19) in Upper Respiratory Samples
Authors: Wang Hannah , Hogan Catherine A , Verghese Michelle , Solis Daniel , Sibai Mamdouh , Huang ChunHong , Zehnder James , Sahoo Malaya K , Pinsky Benjamin A 
Published: April 2021

Abstract
An ultra-sensitive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid antigen assay (S-PLEX, MesoScale Diagnostics) was evaluated in 250 retrospective and 200 prospective upper respiratory specimens. In samples with cycle threshold &lt;35, there was 95%–98% positive and 93%–96% negative percent agreement with reverse transcription-polymerase chain reaction. S-PLEX may provide a high-throughput alternative to nucleic acid-based testing for coronavirus disease 2019 (COVID-19) diagnosis.
The Effect of In-Person Primary and Secondary School Instruction on County-Level Severe Acute Respiratory Syndrome Coronavirus 2 Spread in Indiana
Authors: Bosslet Gabriel T , Pollak Micah , Jang Jeong Hoon , Roll Rebekah , Sperling Mark , Khan Babar 
Published: April 2021

Abstract

Background
Our goal was to determine the county-level effect of in-person primary and secondary school reopening on daily cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Indiana.

Methods
In this county-level, population-based study, we used a panel data regression analysis of the proportion of in-person learning to evaluate an association with community-wide daily new SARS-CoV-2 cases. The study period was 12 July 2020–6 October 2020. We included 73 of 92 (79.3%) Indiana counties in the analysis, accounting for 85.7% of school corporations and 90.6% of student enrollment statewide. The primary exposure was the proportion of students returning to in-person instruction. The primary outcome was the daily new SARS-CoV-2 cases per 100 000 residents at the county level.

Results
There is a statistically significant relationship between the proportion of students attending K-12 schools in-person and the county level daily cases of SARS-CoV-2 28 days later. For all ages, the coefficient of interest (β) is estimated at 3.36 (95% confidence interval, 1.91 to 4.81; P &lt; .001). This coefficient represents the effect of a change in the proportion of students attending in-person on new daily cases 28 days later. For example, a 10 percentage point increase in K-12 students attending school in-person is associated with a daily increase in SARS-CoV-2 cases in the county equal to 0.336 cases/100 000 residents of all ages.

Conclusions
In-person primary and secondary school is associated with a statistically significant but proportionally small increase in the spread of SARS-CoV-2 cases.
Post-translational modifications in proteins: resources, tools and prediction methods
Authors: Ramazi Shahin , Zahiri Javad 
Published: April 2021

Abstract
Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.
Selective perimeter lockdowns in Madrid: a way to bend the COVID-19 curve?
Authors: Fontán-Vela Mario , Gullón Pedro , Padilla-Bernáldez Javier 
Published: April 2021

Abstract
Lockdowns have been widespread used to limit social interaction and bend the epidemic curve. However, their intensity and geographical delimitation have been variable across different countries. Madrid (Spain) implemented perimeter lockdowns in September with the purpose of bending the COVID-19 curve. In this article, we compared, using join point regressions, the evolution of COVID-19 cases in those areas where this intervention was implemented and those where it was not. According to our analysis, the decrease in the epidemic curve started before the impact of the perimeter lockdown could be reflected.
‘I was scared I will end up in another abortion’: a mixed-methods study assessing the impact of COVID-19 pandemic and lockdown on the antenatal care of pregnant women in Puducherry, South India
Authors: Ulaganeethi Revathi , Dorairajan Gowri , Ramaswamy Gomathi , Thekkur Pruthu , Olickal Jeby Jose , Rajkumari Nonika , Kumar Saya Ganesh 
Published: April 2021

Abstract

Background
As a mitigation measure for COVID-19 pandemic, lockdown was implemented in India for a period of 2 months (24 March–31 May 2020). Disruption in antenatal care (ANC) provisions during lockdown is expected due to diversion of public health facilities on pandemic.

Objective
To assess the proportion of pregnant women who had not completed the ideal number of antenatal visits, availability of iron–folic acid (IFA) supplements and challenges in availing health services during the period of lockdown.

Methods
A concurrent mixed-methods study was conducted among pregnant women in Puducherry, India. Information on obstetric characteristics and details regarding antenatal visits were collected through telephonic interviews. In-depth interviews were conducted to understand the perceived challenges in availing health services during the lockdown period.

Results
Out of 150 pregnant women, 62 [41.3%; 95% confidence interval (CI) 33.6–49.3] did not complete the ideal number of visits and 61 (40.7%, 95% CI 32.7–49.0) developed health problems. Out of 44 women who received medical care for health problems, 11 (25%) used teleconsultation. Of all the women, 13 (8.7%, 95% CI 4.9–14.0) had not taken the IFA supplements as prescribed by the health provider. Economic hardship, restricted mobility, lack of information about the health system changes and psychological stress due to the fear of COVID were the challenges in accessing care.

Conclusions
Two out of five pregnant women did not complete the ideal number of visits and developed health problems during the lockdown period.
Upper airway cough syndrome may be the main cause of chronic cough in Japan: a cohort study
Authors: Yasuda Kimihiko 
Published: April 2021

Abstract

Background
Upper airway cough syndrome (UACS) is generally considered a common cause of chronic cough but remains poorly recognised in Japan.

Objective
This study aimed to assess whether UACS was a common cause of chronic cough in Japan, as is true in other countries. Interview and examination items were evaluated for their potential use in UACS diagnosis.

Methods
All patients with chronic cough were preliminarily diagnosed with bronchial asthma, UACS, gastroesophageal reflux disease, or postinfectious prolonged cough, based on interviews and examinations. Treatment centred on nasal steroids was administered to the UACS group and standard treatment to the other groups. The observation period lasted 4 weeks. The subjective cough score at first diagnosis was set at 10, and the final diagnosis was made based on the treatment administered at the time the cough score had decreased to ≤2. The associations between the presence or absence of UACS and interview and examination items were statistically evaluated.

Results
Among 230 patients with chronic cough, 146 were diagnosed with UACS-only. Multivariate logistic regression revealed that the assessment items ‘awareness of mucus accumulating in the back of the throat’, ‘presence of abnormal echography findings’, ‘absence of associated coughing when exercising’ and ‘presence of coughing persisting after onset’ were significantly correlated with the presence or absence of UACS (p &lt; 0.05).

Conclusions
UACS may be the most common cause of chronic cough in Japan and may be effectively treated with nasal corticosteroids. Diagnosing UACS might be possible by selecting appropriate interview and examination items.
Isolation, identification and some characteristics of two lytic bacteriophages against Salmonella enterica serovar Paratyphi B and S. enterica serovar Typhimurium from various food sources
Authors: Sabzali Somaieh , Bouzari Majid 
Published: April 2021

ABSTRACT
Salmonellosis is an important worldwide food-borne disease. Increasing resistance to Salmonella spp. has been reported in recent years, and now the prevalence of multidrug-resistant Salmonella spp. is a worldwide problem. This necessitates alternative approaches like phage therapy. This study aimed to isolate bacteriophages specific for Salmonella enterica serovar Paratyphi B and S. enterica serovar Typhimurium isolated from different sources (chicken meat, beef and eggshells). The antibiotic resistance profiles of the bacteria were determined by phenotypic and genotypic methods. The prevalence of extended-spectrum β-lactamase genes was examined by polymerase chain reaction. In total, 75% of the isolated Salmonella strains were resistant to tetracycline, whereas 70% of them were resistant to azithromycin. All of the isolates from beef were resistant to nalidixic acid. The most common extended-spectrum β-lactamase genes among the isolates were blaSHV (15%) followed by blaTEM (10%) and blaCTX (5%). Two specific bacteriophages were isolated and characterized. The host range for vB_SparS-ui was Salmonella Paratyphi B, S. enterica serovar Paratyphi A and S. enterica, while that for vB_StyS-sam phage was Salmonella Typhimurium and S. enterica serovar Enteritidis. The characteristics of the isolated phages indicate that they are proper candidates to be used to control some foodstuff contaminations and also phage therapy of infected animals.
Inactivation of the Neurospora crassa gene encoding the mitochondrial protein import receptor MOM19 by the technique of "sheltered RIP".
Authors: Harkness T A , Metzenberg R L , Schneider H , Lill R , Neupert W , Nargang F E 
Published: April 2021

Abstract
We have used a technique referred to as "sheltered RIP" (repeat induced point mutation) to create mutants of the mom-19 gene of Neurospora crassa, which encodes an import receptor for nuclear encoded mitochondrial precursor proteins. Sheltered RIP permits the isolation of a mutant gene in one nucleus, even if that gene is essential for the survival of the organism, by sheltering the nucleus carrying the mutant gene in a heterokaryon with an unaffected nucleus. Furthermore, the nucleus harboring the RIPed gene contains a selectable marker so that it is possible to shift nuclear ratios in the heterokaryons to a state in which the nucleus containing the RIPed gene predominates in cultures grown under selective conditions. This results in a condition where the target gene product should be present at very suboptimal levels and allows the study of the mutant phenotype. One allele of mom-19 generated by this method contains 44 transitions resulting in 18 amino acid substitutions. When the heterokaryon containing this allele was grown under conditions favoring the RIPed nucleus, no MOM19 protein was detectable in the mitochondria of the strain. Homokaryotic strains containing the RIPed allele exhibit a complex and extremely slow growth phenotype suggesting that the product of the mom-19 gene is important in N. crassa.
Genetic analysis of male reproductive contributions in Chamaelirium luteum (L.) gray (Liliaceae).
Authors: Smouse P E , Meagher T R 
Published: April 2021

Abstract
Genealogical analysis is a powerful tool for analysis of reproductive performance in both natural and captive populations, but assignment of paternity has always been a stumbling block for this sort of work. Statistical methods for determining paternity have undergone several phases of development, ranging from straightforward genetic exclusion to assignment of paternity based on genetic likelihood criteria. In the present study, we present a genetic likelihood-based iterative procedure for fractional allocation of paternity within a progeny pool and apply this method to a population of Chamaelirium luteum, a dioecious member of the Liliaceae. Results from this analysis clearly demonstrate that different males make unequal contributions to the overall progeny pool, with many males contributing essentially nothing to the next generation. Furthermore, the distribution of paternal success among males shows a highly significant departure from (Poisson) randomness. The results from the present analysis were compared with earlier results obtained from the same data set, using likelihood-based categorical paternity assignments. The general biological pattern revealed by the two analyses is the same, but the estimates of reproductive success are only modestly (though significantly) correlated. The iterative procedure makes more complete use of the data and generates a more sharply resolved distribution of male reproductive success.
Possible role of natural selection in the formation of tandem-repetitive noncoding DNA.
Authors: Stephan W , Cho S 
Published: April 2021

Abstract
A simulation model of sequence-dependent amplification, unequal crossing over and mutation is analyzed. This model predicts the spontaneous formation of tandem-repetitive patterns of noncoding DNA from arbitrary sequences for a wide range of parameter values. Natural selection is found to play an essential role in this self-organizing process. Natural selection which is modeled as a mechanism for controlling the length of a nucleotide string but not the sequence itself favors the formation of tandem-repetitive structures. Two measures of sequence heterogeneity, inter-repeat variability and repeat length, are analyzed in detail. For fixed mutation rate, both inter-repeat variability and repeat length are found to increase with decreasing rates of (unequal) crossing over. The results are compared with data on micro-, mini- and satellite DNAs. The properties of minisatellites and satellite DNAs resemble the simulated structures very closely. This suggests that unequal crossing over is a dominant long-range ordering force which keeps these arrays homogeneous even in regions of very low recombination rates, such as at satellite DNA loci. Our analysis also indicates that in regions of low rates of (unequal) crossing over, inter-repeat variability is maintained at a low level at the expense of much larger repeat units (multimeric repeats), which are characteristic of satellite DNA. In contrast, the microsatellite data do not fit the proposed model well, suggesting that unequal crossing over does not act on these very short tandem arrays.
Drosophila genetics in the classroom.
Authors: Sofer W , Tompkins L 
Published: April 2021

Abstract
Drosophila has long been useful for demonstrating the principles of classical Mendelian genetics in the classroom. In recent years, the organism has also helped students understand biochemical and behavioral genetics. In this connection, this article describes the development of a set of integrated laboratory exercises and descriptive materials--a laboratory module--in biochemical genetics for use by high-school students. The module focuses on the Adh gene and its product, the alcohol dehydrogenase enzyme. Among other activities, students using the module get to measure alcohol tolerance and to assay alcohol dehydrogenase activity in Adh-negative and -positive flies. To effectively present the module in the classroom, teachers attend a month-long Dissemination Institute in the summer. During this period, they learn about other research activities that can be adapted for classroom use. One such activity that has proved popular with teachers and students utilizes Drosophila to introduce some of the concepts of behavioral genetics to the high-school student. By establishing closer interactions between high-school educators and research scientists, the gulf between the two communities can begin to be bridged. It is anticipated that the result of a closer relationship will be that the excitement and creativity of science will be more effectively conveyed to students.
The SPT10 and SPT21 genes of Saccharomyces cerevisiae.
Authors: Natsoulis G , Winston F , Boeke J D 
Published: April 2021

Abstract
Mutations in the SPT10 and SPT21 genes were originally isolated as suppressors of Ty and LTR (delta) insertion mutations in Saccharomyces cerevisiae, and the genes were shown to be required for normal transcription at a number of loci in yeast. Now we have cloned, sequenced, mapped and mutagenized SPT10 and SPT21. Since the spt10 mutation used to clone SPT10 resulted in very poor transformation efficiency, a novel method making use of the kar1-1 mutation was used. Neither SPT gene is essential for growth, and constructed null alleles cause phenotypes similar to those caused by spontaneous mutations in the genes. spt10 null alleles are strong suppressor mutations and cause extremely slow growth. Certain spt10 spontaneous alleles are good suppressors but have a normal growth rate, suggesting that the SPT10 protein may have two distinct functions. An amino acid sequence motif that is similar to the Zn-finger motif was found in SPT10. Mutation of the second Cys residue in this motif resulted in loss of complementation of the suppression phenotype but a normal growth rate. Thus, this motif may reside in a part of the SPT10 protein that is important for transcriptional regulation but not for normal growth. Both the SPT10 and SPT21 proteins are relatively tolerant of large deletions; in both cases deletions of the C-terminus resulted in at least partially functional proteins; also, a large internal deletion in SPT21 was phenotypically wild type.