bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minor extensions of the logistic equation for growth curves of word counts on online media: parametric observation of diversity of growth in society
Authors: Watanabe Hayafumi 
Published: May 2023

Abstract
To understand the growth phenomena in collective human systems, we analyzed monthly word count time series of new vocabularies extracted from approximately 1 billion Japanese blog articles from 2007 to 2019. In particular, we first introduced the extended logistic equation by adding one parameter to the original equation and showed that the model can consistently reproduce various patterns of actual growth curves, such as the logistic function, linear growth, and finite-time divergence. Second, by analyzing the model parameters, we found that the typical growth pattern is not only a logistic function, which often appears in various complex systems, but also a non-trivial growth curve that starts with an exponential function and asymptotically approaches a power function without a steady state. We also observed a connection between the functional form of growth and the peak-out behavior. Finally, we showed that the proposed model and statistical properties are also valid for Google Trends data (English, French, Spanish, and Japanese), which is a time series of the nationwide popularity of search queries.
A structure theory for stable codimension 1 integral varifolds with applications to area minimising hypersurfaces mod 𝑝
Authors: Minter Paul , Wickramasekera Neshan 
Published: May 2023

For any

Q
∈
{

3
2

,
2
,

5
2

,
3
,
…
}

Q\in \{\frac {3}{2},2,\frac {5}{2},3,\dotsc \}

, we establish a structure theory for the class

S

Q

\mathcal {S}_Q

of stable codimension 1 stationary integral varifolds admitting no classical singularities of density

>
Q

>Q

. This theory comprises three main theorems which describe the nature of a varifold

V
∈

S

Q

V\in \mathcal {S}_Q

when: (i)

V
V

is close to a flat disk of multiplicity

Q
Q

(for integer

Q
Q

); (ii)

V
V

is close to a flat disk of integer multiplicity

>
Q

>Q

; and (iii)

V
V

is close to a stationary cone with vertex density

Q
Q

and supports the union of 3 or more half-hyperplanes meeting along a common axis. The main new result concerns (i) and gives in particular a description of

V
∈

S

Q

V\in \mathcal {S}_Q

near branch points of density

Q
Q

. Results concerning (ii) and (iii) directly follow from parts of previous work of the second author [Ann. of Math. (2) 179 (2014), pp. 843–1007].

These three theorems, taken with

Q
=
p

/

2

Q=p/2

, are readily applicable to codimension 1 rectifiable area minimising currents mod

p
p

for any integer

p
≥
2

p\geq 2

, establishing local structure properties of such a current

T
T

as consequences of little, readily checked, information. Specifically, applying case (i) it follows that, for even

p
p

, if

T
T

has one tangent cone at an interior point

y
y

equal to an (oriented) hyperplane

P
P

of multiplicity

p

/

2

p/2

, then

P
P

is the unique tangent cone at

y
y

, and

T
T

near

y
y

is given by the graph of a

p
2

\frac {p}{2}

-valued function with

C

1
,
α

C^{1,\alpha }

regularity in a certain generalised sense. This settles a basic remaining open question in the study of the local structure of such currents near points with planar tangent cones, extending the cases

p
=
2

p=2

and

p
=
4

p=4

of the result which have been known since the 1970’s from the De Giorgi–Allard regularity theory [Ann. of Math. (2) 95 (1972), pp. 417–491] [Frontiere orientate di misura minima, Editrice Tecnico Scientifica, Pisa, 1961] and the structure theory of White [Invent. Math. 53 (1979), pp. 45–58] respectively. If

P
P

has multiplicity

>
p

/

2

> p/2

(for

p
p

even or odd), it follows from case (ii) that

T
T

is smoothly embedded near

y
y

, recovering a second well-known theorem of White [Proc. Sympos. Pure Math., Amer. Math. Soc., Providence, RI, 1986, pp. 413–427]. Finally, the main structure results obtained recently by De Lellis–Hirsch–Marchese–Spolaor–Stuvard [arXiv:2105.08135, 2021] for such currents

T
T

all follow from case (iii).
Clinically Occult Diffuse Pleural Mesothelioma in Patients Presenting With Spontaneous Pneumothorax
Authors: Fels Elliott Daffolyn Rachael , Konopka Kristine E , Hrycaj Steven M , Lagisetty Kiran H , Myers Jeffrey L , Farver Carol F , Huang Tao 
Published: May 2023

Abstract

Objectives
To report histologic features of unsuspected diffuse pleural mesothelioma (DPM) in surgical specimens for pneumothorax and demonstrate how ancillary markers support a diagnosis of malignancy in this context. We explored whether pneumothorax may be a clinical manifestation of mesothelioma in situ (MIS).

Methods
A single-institution database search identified patients who underwent surgical resection for spontaneous pneumothorax (n = 229) and/or were diagnosed with DPM (n = 88) from 2000 to 2020.

Results
Spontaneous pneumothorax without clinical, radiologic, or intraoperative suspicion of mesothelioma was the initial presentation in 2 (2.3%) of 88 patients diagnosed with DPM. This represented 0.9% (2/229) of all patients undergoing surgical management of pneumothorax but accounted for a larger proportion of older patients (12.5% older than 70 years). Immunohistochemistry for BAP-1 and/or MTAP confirmed the diagnosis of DPM in 2 cases. Mesothelioma in situ was identified retrospectively by immunohistochemistry in 1 case of spontaneous pneumothorax from a 77-year-old man who developed invasive DPM 25 months later. No additional cases of MIS were identified in 19 surgical lung resections for spontaneous pneumothorax.

Conclusions
Histologic examination of bleb resections with ancillary testing for cases with ambiguous features is essential for detection of early DPM. It is uncertain whether spontaneous pneumothorax may represent a clinical manifestation of MIS.
Evaluation of a novel blood volume–based enoxaparin dosing guideline for venous thromboembolism prophylaxis in trauma patients
Authors: Langenstroer Elizabeth A , Carver Thomas W , Herrmann David J , O’Keefe Mary M , Hubbard Sara , Holschbach Leah , Rein Lisa , Peppard William J 
Published: May 2023

Abstract

Purpose
Fixed-dose and body mass index (BMI)–based enoxaparin regimens provide inadequate venous thromboembolism (VTE) prophylaxis for many trauma patients. The purpose of this study was to evaluate the effectiveness of a novel blood volume (BV)–based enoxaparin guideline vs a historical BMI-based guideline for VTE prophylaxis in trauma patients.

Methods
This was a retrospective pre/post study completed at a large academic level 1 trauma center. All adult trauma patients admitted from October through December 2019 and August through October 2020 who received prophylactic enoxaparin per guideline were included. The BV dosing was as follows: patients with a BV of 3 to 4.9 L received enoxaparin 30 mg every 12 hours, those with a BV of 5 to 6.9 L received 40 mg every 12 hours, and those with a BV of ≥7 L received 60 mg every 12 hours. The primary outcome was the percentage of patients who attained a target anti–factor Xa (anti-Xa) postdosing level at the first steady-state assessment (0.2 to 0.5 IU/mL).

Results
A total of 241 patients (99 for the BMI group and 142 for the BV group) were included. The study groups had a median age of 38 vs 42 years, a mean BMI of 27.4 vs 27.7 kg/m2, and a mean BV of 5.1 vs 5.1 L, respectively. A total of 63 patients (62.6%) in the BMI group attained target anti-Xa levels compared to 115 patients (81%) in the BV group (P = 0.008). In multivariate regression, the BV-based guideline was the only variable associated with attainment of target anti-Xa levels (adjusted odds ratio, 2.02; P = 0.01). Clinically relevant bleeding and VTE rates were similar between the groups.

Conclusion
Dosing prophylactic enoxaparin using a BV-based dosing guideline significantly increased attainment of target anti-Xa levels.
MITNet: a fusion transformer and convolutional neural network architecture approach for T-cell epitope prediction
Authors: Darmawan Jeremie Theddy , Leu Jenq-Shiou , Avian Cries , Ratnasari Nanda Rizqia Pradana 
Published: May 2023

Abstract
Classifying epitopes is essential since they can be applied in various fields, including therapeutics, diagnostics and peptide-based vaccines. To determine the epitope or peptide against an antibody, epitope mapping with peptides is the most extensively used method. However, this method is more time-consuming and inefficient than using present methods. The ability to retrieve data on protein sequences through laboratory procedures has led to the development of computational models that predict epitope binding based on machine learning and deep learning (DL). It has also evolved to become a crucial part of developing effective cancer immunotherapies. This paper proposes an architecture to generalize this case since various research strives to solve a low-performance classification problem. A proposed DL model is the fusion architecture, which combines two architectures: Transformer architecture and convolutional neural network (CNN), called MITNet and MITNet-Fusion. Combining these two architectures enriches feature space to correlate epitope labels with the binary classification method. The selected epitope–T-cell receptor (TCR) interactions are GILG, GLCT and NLVP, acquired from three databases: IEDB, VDJdb and McPAS-TCR. The previous input data was extracted using amino acid composition, dipeptide composition, spectrum descriptor and the combination of all those features called AADIP composition to encode the input data to DL architecture. For ensuring consistency, fivefold cross-validations were performed using the area under curve metric. Results showed that GILG, GLCT and NLVP received scores of 0.85, 0.87 and 0.86, respectively. Those results were compared to prior architecture and outperformed other similar deep learning models.
PPIntegrator: semantic integrative system for protein–protein interaction and application for host–pathogen datasets
Authors: Martins Yasmmin Côrtes , Ziviani Artur , Cerqueira e Costa Maiana de Oliveira , Cavalcanti Maria Cláudia Reis , Nicolás Marisa Fabiana , de Vasconcelos Ana Tereza Ribeiro 
Published: May 2023

Abstract

Summary
Semantic web standards have shown importance in the last 20 years in promoting data formalization and interlinking between the existing knowledge graphs. In this context, several ontologies and data integration initiatives have emerged in recent years for the biological area, such as the broadly used Gene Ontology that contains metadata to annotate gene function and subcellular location. Another important subject in the biological area is protein–protein interactions (PPIs) which have applications like protein function inference. Current PPI databases have heterogeneous exportation methods that challenge their integration and analysis. Presently, several initiatives of ontologies covering some concepts of the PPI domain are available to promote interoperability across datasets. However, the efforts to stimulate guidelines for automatic semantic data integration and analysis for PPIs in these datasets are limited. Here, we present PPIntegrator, a system that semantically describes data related to protein interactions. We also introduce an enrichment pipeline to generate, predict and validate new potential host–pathogen datasets by transitivity analysis. PPIntegrator contains a data preparation module to organize data from three reference databases and a triplification and data fusion module to describe the provenance information and results. This work provides an overview of the PPIntegrator system applied to integrate and compare host–pathogen PPI datasets from four bacterial species using our proposed transitivity analysis pipeline. We also demonstrated some critical queries to analyze this kind of data and highlight the importance and usage of the semantic data generated by our system.

Availability and implementation
https://github.com/YasCoMa/ppintegrator, https://github.com/YasCoMa/ppi_validation_process and https://github.com/YasCoMa/predprin.
Regulation of uterus and placenta remodeling under high estradiol levels in gestational diabetes mellitus models
Authors: Kang Da Hee , Kim Min Jae , Mohamed Elsayed A , Kim Da Som , Jeong Jea Sic , Kim So Young , Kang Hyeon-Gu , Lee Geun-Shik , Hong Eui-Ju , Ahn Changhwan , Jung Eui-Man , An Beum-Soo , Kim Seung-Chul 
Published: May 2023

Abstract
The present study aimed to investigate the regulation of placentas and uterus remodeling and involvement of estradiol in gestational diabetes mellitus. To achieve this, we established in vitro and in vivo models for gestational diabetes mellitus placentas by culturing human placental choriocarcinoma cells (BeWo) under hyperglycemic concentration and treating pregnant rats with streptozotocin. We evaluated the expression of angiogenesis-related proteins. The expression of the anti-angiogenic factor, excess placental soluble fms-like tyrosine kinase 1 was increased in our in vitro gestational diabetes mellitus model compared with the control. Moreover, the expressions of placental soluble fms-like tyrosine kinase 1 and the von Willebrand factor were also significantly elevated in the placenta of streptozotocin-treated rats. These data indicate the disruption of angiogenesis in the gestational diabetes mellitus placentas. The expression levels of connexin 43, a component of the gap junction and collagen type I alpha 2 chain, a component of the extracellular matrix, were decreased in the gestational diabetes mellitus uterus. These results suggest that uterus decidualization and placental angiogenesis are inhibited in gestational diabetes mellitus rats. Our results also showed upregulation of the expression of genes regulating estradiol synthesis as well as estrogen receptors in vivo models. Accordingly, the concentration of estradiol measured in the culture medium under hyperglycemic conditions, as well as in the serum and placenta of the streptozotocin-treated rats, was significantly elevated compared with the control groups. These results suggest that the dysregulated remodeling of the placenta and uterus may result in the elevation of estradiol and its signaling pathway in the gestational diabetes mellitus animal model to maintain pregnancy.
Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches
Authors: Li Xiongwei , Wang Jiabo , Su Mingshen , Zhang Minghao , Hu Yang , Du Jihong , Zhou Huijuan , Yang Xiaofeng , Zhang Xianan , Jia Huijuan , Gao Zhongshan , Ye Zhengwen 
Published: May 2023

Abstract
‘Chinese Cling’ is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the ‘Shanghai Shuimi’ landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.
Impact of Human Papillomavirus Vaccine Against Anal Human Papillomavirus Infection, Anal Intraepithelial Neoplasia, and Recurrence of Anal Intraepithelial Neoplasia: A Systematic Review and Meta-analysis
Authors: Wei Feixue , Alberts Catharina J , Albuquerque Andreia , Clifford Gary M 
Published: May 2023

Abstract

Background
We sought to summarize human papillomavirus (HPV) vaccine efficacy/effectiveness (VE) against anal HPV infection and anal intraepithelial neoplasia (AIN).

Methods
We performed literature review and meta-analysis to estimate VE, stratified by age and analytic population (per-protocol efficacy [PPE] or intention-to-treat [ITT] population in clinical trials, or all participants in real-world studies).

Results
We identified 6 clinical trials and 8 real-world studies. In participants vaccinated at age ≤26 years (mainly human immunodeficiency virus [HIV]–negative individuals), significant VE against incident/prevalent anal HPV infection was reported in clinical trials, with a higher estimate in PPE (2 studies with 2390 participants; VE, 84% [95% confidence interval (CI), 77%–90%]; I2 = 0%) than ITT (2 studies with 4885 participants; 55%, 39%–67%; I2 = 46%) populations or in real-world studies (4 studies with 2375 participants; 77%, 40%–91%; I2 = 81%). HPV vaccination at age ≤26 years was associated with significant VE in preventing persistent anal HPV infection and AIN. No significant VE against anal HPV infection or AIN was found in persons vaccinated at age &gt;26 years (mainly people living with HIV).

Conclusions
There is strong evidence for high VE against anal HPV infection and AIN in HIV-negative individuals vaccinated at age ≤26 years. However, the lower impact in ITT than in PPE populations and the lack of significant effect in people living with HIV aged &gt;26 years indicates that vaccines have the higher impact in populations with less sexual exposure to anal HPV.
Canadian records of Branchinecta serrata Rogers, 2006 and its confusion with B. paludosa (Müller, 1788) (Branchiopoda: Anostraca: Branchinectidae), with a key to the B. paludosa species group
Authors: Rogers D Christopher , Gardiner Ian R 
Published: May 2023

Abstract
Branchinecta serrata Rogers, 2006 was originally thought to be limited to four localities in the central USA. We present new records of this species in prairie pools in central Canada, greatly extending its known distribution. Previous records from Canada were misidentified as the common and widespread B. paludosa (Müller, 1788). We present images emphasizing the differences between the two species, updated geochemical tolerance data, and revise the conservation status of B. serrata. Finally, we present an identification key to the Branchinecta paludosa species group.
Keeping Up with Current Practices in a Rapidly Evolving Field Through Dissemination of “Tips and Tricks” in a Monthly Webinar
Authors: Zimanyi Christina M , Rayaprolu Vamseedhar 
Published: May 2023

Abstract
In the past decade, cryo-electron microscopy (cryoEM) has become a vital tool for structural biologists. Using cryoEM to determine structures of biomolecules at high resolution is a rapidly evolving technique with high barriers to entry for non-microscopists. To help academic researchers remain competitive in their fields, the NIH established a network of centers to broaden access and training in cryoEM. One initiative from this network is the monthly CryoEM Current Practices webinar that provides practical methodological tips and tricks and is openly accessible to anyone interested. Now in its third year, the webinar continues to attract a sizable audience and provides a forum for network building within the structural biology community.
Using Antibodies in Microscopy: A Guide to Immunohistochemistry. Part 2: IHC Staining Protocols
Authors: Guerin Christopher J 
Published: May 2023

Abstract
Immunohistochemistry (IHC) is the use of antibodies as probes to determine the localization of proteins in a cell or tissue sample. In microscopy, the technique has been in use since the 1940s by pathologists and research scientists. At first glance it appears a straightforward procedure. However, in practice, an IHC protocol has a number of steps where problems can occur, resulting in either false positive or false negative data. IHC can be used in both transmitted light and fluorescence microscopy, and it can be used in combinations to identify and mark multiple proteins of interest. While the technique has been published extensively, a certain amount of confusion exists as to how to optimize it. This series of three articles describes the steps involved in IHC, their function, and some variations that occur in specific protocols on differing cell and tissue types. It is hoped that a better understanding of these steps will help to guide users in determining the optimal conditions for carrying through IHC protocols.
Survival of U.S. Military Service Members With Lymphoma
Authors: Ancira Gilbert , Romain Joshua , Pham Kevin , Thornton Jennifer A , DeStefano Christin B 
Published: May 2023

ABSTRACT

Introduction
Cancer is a prominent cause of mortality in today’s active duty service members (ADSMs), killing over 700 ADSMs between 2004 and 2015. Hence, more research is needed to better understand the survival of U.S. service members with cancer. Lymphoma is the most common hematologic malignancy diagnosed in ADSMs, serving as a good cancer type to study.

Materials and Methods
The Department of Defense tumor registry and the Surveillance, Epidemiology, and End Result (SEER) databases were retrospectively accessed to analyze overall survival (OS) of ADSMs with lymphoma and to compare outcomes with matched civilians. ADSMs with Hodgkin lymphoma (HL), diffuse large B-cell lymphoma (DLBCL), and indolent lymphoma diagnosed between 1997 and 2017 were included, and SEER comparator patients were matched by age, sex, race, stage, and year of diagnosis using a 4:1 ratio of civilians to ADSMs.

Results
There were 1,170, 443, and 284 ADSMs with HL, DLBCL, and indolent lymphoma, respectively, and all three groups had superior OS when compared to their matched civilian counterparts with 35%, 49%, and 48% reductions in the risk of death, respectively. There were no differences in ADSM survival based on race, sex, or rank, despite disparities being pervasive in the civilian sector.

Conclusions
Service members with lymphoma have superior survival than their matched civilian counterparts, without evident racial or sex disparities. Results of this study are favorable in terms of readiness. Further research on cancer mortality in ADSMs is needed to improve long-term outcomes.
The role of student effort on performance in PISA: revisiting the gender gap in achievement
Authors: Anaya Lina M , Zamarro Gema 
Published: May 2023

Abstract
International assessments are important to benchmark the quality of education internationally. However, ignoring students’ efforts in low-stakes tests can lead to biased interpretations of test performance. We use data from the PISA to analyse the potential role of student effort in explaining gender achievement gaps across countries. We build two effort measures based on students’ response times to test questions (i.e. rapid-guessing rates) and the student effort on the post-test survey (i.e. item non-response rates). We find a strong association between student efforts and test scores. After accounting for differences in effort, the estimated gender achievement gap in mathematics and science could be up to 36% and 40% of an standard deviation wider, respectively, in favour of boys. Altogether, our effort measures on average explain between 51% and 56% of the cross-country variation in test scores.