bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anal High-risk HPV and Liquid-based Cytology of Immunocompetent Brazilian Women with Genital High-risk HPV
Authors: Melo Karla Maria Rêgo Leopoldo , Eleutério Junior José , Peixoto Raquel Autran Coelho , Rebouças Karinne Cisne Fernandes , Eleutério Renata Mirian Nunes 
Published: February 2022

Abstract
Objective The purpose of this study was to compare the frequency of the occurrence of high-risk human papillomavirus (HPV) and abnormal anal cytology in immunocompetent women with and without HPV-induced genital lesions.
Methods This analytical cross-sectional, observational study was conducted between July 2017 and December 2018 in a specialized outpatient clinic of a tertiary hospital in Fortaleza, CE. Fifty-seven immunocompetent women with and without genital intraepithelial lesions were assessed; they were divided into two groups: group 1 was comprised of women with HPV-associated genital lesions (n = 26), and group 2 was comprised of those without HPV-associated genital lesions (n = 31). Samples for liquid-based cytology and high-risk DNA-HPV polymerase chain reaction real-time tests were collected from the cervix and anus. All cases were evaluated using high-resolution anoscopy; biopsies were performed when required. The Fisher exact and chi-squared tests were applied for consolidated data in the contingency table, and the Student t-test and Mann-Whitney U-test for independent variables.
Results Anal high-risk HPV infections were more frequent in group 1 (odds ratio [OR], 4.95; 95% confidence interval [CI], 1.34–18.3; p = 0.012), along with concomitant high-risk HPV infections in the uterine cervix and the anus (OR 18.8; 95% CI, 2.20–160; p < 0.001). The incidence of high-risk cervical HPV infection was associated with high-risk anal HPV infection (OR, 4.95; 95% CI, 1.34–18.3; p = 0.012). There was no statistical difference concerning abnormal anal cytology or anoscopy between the groups, and no anal intraepithelial lesion was found in either group.
Conclusion Immunocompetent women with HPV-associated genital lesions and high-risk cervical HPV were more likely to have high-risk anal HPV.
The associations between motivational climate, basic psychological needs and dropout in volleyball – A comparison across competitive levels
Authors: Elsborg Peter , Appleton Paul , Wikman Johan M. , Nielsen Glen 
Published: February 2022

ABSTRACTThe purpose of this study was to investigate the importance of motivational climate for the satisfaction of psychological needs and dropout in recreational, intermediate and elite volleyball. Seven thousand nine hundred thirty six volleyball players from all 321 volleyball clubs across Denmark were invited to participate in the study. Three thousand three thirty answered the questionnaire and 2150 were included in the analysis. Dropout from Volleyball was measured as the proportion of players that had stopped playing volleyball over the last year. The coach‐created motivational climate was measured using the Motivational Climate Scale for Youth Sports. The satisfaction of players’ psychological needs was measured using an adapted version of the basic psychological needs in exercise scale. The psychometric scales were validated and showed good model fit. For volleyball players of all levels, the degree of mastery climate predicted the satisfaction of the players’ basic psychological needs satisfaction during volleyball which was, in turn, associated with lower dropout rates. Performance climate had a weak negative association with the satisfaction of psychological needs on the intermediate level only. When adjusting the models for the negative association between performance climate and mastery climate this negative association became nonsignificant and a weak positive association to needs satisfaction emerged for players at the elite level. Findings confirm that the coach‐created mastery climate in volleyball teams is important for the satisfaction of players’ basic psychological needs and continuation within the sport across the recreational, intermediate and elite levels.

Highlights
Coach‐created mastery climate in volleyball teams was positively associated with the satisfaction of the players’ basic psychological and negatively associated with dropout.
These associations between coach created climate, need satisfaction and dropout were similar across different sporting levels.
Performance orientation had little influence and seemed mainly problematic if it was at the expense of mastery climate.
Spin correlation functions, Ramus-like identities, and enumeration of constrained lattice walks and plane partitions
Authors: Malyshev C , Bogoliubov N M 
Published: February 2022

Abstract
Relations between the mean values of distributions of flipped spins on periodic Heisenberg XX chain and some aspects of enumerative combinatorics are discussed. The Bethe vectors, which are the state-vectors of the model, are considered both as on- and off-shell. It is this approach that makes it possible to represent and to study the correlation functions in the form of non-intersecting nests of lattice walks and related plane partitions. We distinguish between two types of walkers, namely lock step models and random turns. Of particular interest is the connection of random turns walks and a circulant matrix. The determinantal representation for the norm-trace generating function of plane partitions with fixed height of diagonal parts is obtained as the expectation of the generating exponential over off-shell N-particle Bethe states. The asymptotics of the dynamical mean value of the generating exponential is calculated in the double scaling limit provided that the evolution parameter is large. It is shown that the amplitudes of the leading asymptotics depend on the number of diagonally constrained plane partitions.
Improvements of 𝑝-adic estimates of exponential sums
Authors: Feng Yulu , Hong Shaofang 
Published: February 2022

Let

n
,
r

n, r

and

f
f

be positive integers. Let

p
p

be a prime number and

ψ
\psi

be an arbitrary fixed nontrivial additive character of the finite field

F

q

\mathbb F_q

with

q
=

p
f

q=p^f

elements. Let

F
F

be a polynomial in

F

q

[

x
1

,
…
,

x
n

]

\mathbb F_q[x_1,\dots ,x_n]

and

V
V

be the affine algebraic variety defined over

F

q

\mathbb {F}_q

by the simultaneous vanishing of the polynomials

{

F
i

}

i
=
1

r

⊆

F

q

[

x
1

,
…
,

x
n

]

\{F_i\}_{i=1}^r\subseteq \mathbb F_q[x_1,\dots ,x_n]

. Let

Z

≥
0

\mathbb {Z}_{\ge 0}

stand for the set of all nonnegative integers and

A
A

be an arbitrary nonempty subset of

{
1
,
…
,
n
}

\{1,\dots ,n\}

. For a polynomial

H
(
X
)
=

∑

d

α

d

X

d

H(X)=\sum _{{\mathbf {d}}}\alpha _{\mathbf {d}}X^{\mathbf {d}}

with

d

=
(

d
1

,
…
,

d
n

)
∈

Z

≥
0

n

,

X

d

=

x
1

d
1

…

x
n

d
n

{\mathbf {d}}=(d_1,\dots ,d_n)\in \mathbb {Z}_{\ge 0}^n, X^{\mathbf {d}}=x_1^{d_1}\dots x_n^{d_n}

and

α

d

∈

F

q
∗

\alpha _{\mathbf {d}}\in \mathbb {F}_q^*

, we define

deg
A

⁡
(
H
)
=

max

d

{

∑

i
∈
A

d
i

}

\deg _A(H)=\max _{{\mathbf {d}}}\{\sum _{i\in A}d_i\}

to be the

A
A

-degree of

H
H

. In this paper, for the exponential sum

S
(
F
,
V
,
ψ
)
=

∑

X
∈
V
(

F

q

)

ψ
(
F
(
X
)
)

S(F,V,\psi )=\sum _{X\in V(\mathbb {F}_q)}\psi (F(X))

with

V
(

F

q

)

V(\mathbb {F}_q)

being the set of the

F

q

\mathbb {F}_q

-rational points of

V
V

, we show that

o
r
d

q

S
(
F
,
V
,
ψ
)
≥

|

A

|

−

∑

i
=
1

r

deg
A

⁡
(

F
i

)

max

1
≤
i
≤
r

{

deg
A

⁡
(
F
)
,

deg
A

⁡
(

F
i

)
}

\begin{equation*} \mathrm {ord}_q S(F,V,\psi )\ge \frac {|A|-\sum _{i=1}^r\deg _A(F_i)} {\max _{1\le i\le r}\{\deg _A(F),\deg _A(F_i)\}} \end{equation*}

if

deg
A

⁡
(
F
)
>
0

\deg _A(F)>0

or

deg
A

⁡
(

F
i

)
>
0

\deg _A(F_i)>0

for some

i
∈
{
1
,
…
,
r
}

i\in \{1,\dots ,r\}

. This estimate improves Sperber’s theorem obtained in 1986. This also leads to an improvement of the

p
p

-adic valuation of the number

N
(
V
)

N(V)

of

F

q

\mathbb {F}_q

-rational points on the variety

V
V

which strengthens the Ax-Katz theorem. Moreover, we use the

A
A

-degree and

p
p

-weight

A
A

-degree to establish

p
p

-adic estimates on multiplicative character sums and twisted exponential sums which improve Wan’s results gotten in 1995.
Detecting drug diversion in health-system data using machine learning and advanced analytics
Authors: Knight Tom , May Bernie , Tyson Don , McAuley Scott , Letzkus Pam , Enright Sharon Murphy 
Published: February 2022

Abstract

Purpose
The theft of drugs from healthcare facilities, also known as drug diversion, occurs frequently but is often undetected. This paper describes a research study to develop and test novel drug diversion detection methods. Improved diversion detection and reduction in diversion improves patient safety, limits harm to the person diverting, reduces the public health impact of substance use disorder, and mitigates significant liability risk to pharmacists and their organizations.

Methods
Ten acute care inpatient hospitals across 4 independent health systems extracted 2 datasets from various health information technology systems. Both datasets were consolidated, normalized, classified, and sampled to provide a harmonious dataset for analysis. Supervised machine learning methods were iteratively used on the initial sample dataset to train algorithms to classify medication movement transactions as involving a low or high risk of diversion. Thereafter, the resulting machine learning model classified the risk of diversion in a historical dataset capturing 8 to 24 months of history that included 27.9 million medication movement transactions by 19,037 nursing, 1,047 pharmacy, and 712 anesthesia clinicians and that included 22 known, blinded diversion cases to measure when the model would have detected the diversion compared to when the diversion was actually detected by existing methods.

Results
The machine learning model had 96.3% accuracy, 95.9% specificity, and 96.6% sensitivity in detecting transactions involving a high risk of diversion using the initial sample dataset. In subsequent testing using the much larger historical dataset, the analytics detected known diversion cases (n = 22) in blinded data faster than existing detection methods (a mean of 160 days and a median of 74 days faster; range, 7-579 days faster).

Conclusion
The study showed that (1) consolidated datasets and (2) supervised machine learning can detect known diversion cases faster than existing detection methods. Users of the technology also noted improved investigation efficiency.
Improving the specificity of drug-drug interaction alerts: Can it be done?
Authors: Reese Thomas , Wright Adam , Liu Siru , Boyce Richard , Romero Andrew , Del Fiol Guilherme , Kawamoto Kensaku , Malone Daniel 
Published: February 2022

Abstract

Purpose
Inaccurate and nonspecific medication alerts contribute to high override rates, alert fatigue, and ultimately patient harm. Drug-drug interaction (DDI) alerts often fail to account for factors that could reduce risk; further, drugs that trigger alerts are often inconsistently grouped into value sets. Toward improving the specificity of DDI alerts, the objectives of this study were to (1) highlight the inconsistency of drug value sets for triggering DDI alerts and (2) demonstrate a method of classifying factors that can be used to modify the risk of harm from a DDI.

Methods
This was a proof-of-concept study focused on 15 well-known DDIs. Using 3 drug interaction references, we extracted 2 drug value sets and any available order- and patient-related factors for each DDI. Fleiss’ kappa was used to measure the consistency of value sets among references. Risk-modifying factors were classified as order parameters (eg, route and dose) or patient characteristics (eg, comorbidities and laboratory results).

Results
Seventeen value sets (56%) had nonsignificant agreement. Agreement among the remaining 13 value sets was on average moderate. Thirty-three factors that could reduce risk in 14 of 15 DDIs (93%) were identified. Most risk-modifying factors (67%) were classified as order parameters.

Conclusion
This study demonstrates the importance of increasing the consistency of drug value sets that trigger DDI alerts and how alert specificity and usefulness can be improved with risk-modifying factors obtained from drug references. It may be difficult to operationalize certain factors to reduce unnecessary alerts; however, factors can be used to support decisions by providing contextual information.
A review of SNP heritability estimation methods
Authors: Tang Mingsheng , Wang Tong , Zhang Xuefen 
Published: February 2022

Abstract
Over the past decade, statistical methods have been developed to estimate single nucleotide polymorphism (SNP) heritability, which measures the proportion of phenotypic variance explained by all measured SNPs in the data. Estimates of SNP heritability measure the degree to which the available genetic variants influence phenotypes and improve our understanding of the genetic architecture of complex phenotypes. In this article, we review the recently developed and commonly used SNP heritability estimation methods for continuous and binary phenotypes from the perspective of model assumptions and parameter optimization. We primarily focus on their capacity to handle multiple phenotypes and longitudinal measurements, their ability for SNP heritability partition and their use of individual-level data versus summary statistics. State-of-the-art statistical methods that are scalable to the UK Biobank dataset are also elucidated in detail.
A survey on the algorithm and development of multiple sequence alignment
Authors: Zhang Yongqing , Zhang Qiang , Zhou Jiliu , Zou Quan 
Published: February 2022

AbstractMultiple sequence alignment (MSA) is an essential cornerstone in bioinformatics, which can reveal the potential information in biological sequences, such as function, evolution and structure. MSA is widely used in many bioinformatics scenarios, such as phylogenetic analysis, protein analysis and genomic analysis. However, MSA faces new challenges with the gradual increase in sequence scale and the increasing demand for alignment accuracy. Therefore, developing an efficient and accurate strategy for MSA has become one of the research hotspots in bioinformatics. In this work, we mainly summarize the algorithms for MSA and its applications in bioinformatics. To provide a structured and clear perspective, we systematically introduce MSA’s knowledge, including background, database, metric and benchmark. Besides, we list the most common applications of MSA in the field of bioinformatics, including database searching, phylogenetic analysis, genomic analysis, metagenomic analysis and protein analysis. Furthermore, we categorize and analyze classical and state-of-the-art algorithms, divided into progressive alignment, iterative algorithm, heuristics, machine learning and divide-and-conquer. Moreover, we also discuss the challenges and opportunities of MSA in bioinformatics. Our work provides a comprehensive survey of MSA applications and their relevant algorithms. It could bring valuable insights for researchers to contribute their knowledge to MSA and relevant studies.
The experimental provision of calcium increases the reproductive success of passerine birds
Authors: Briggs Kevin B , Mainwaring Mark C 
Published: February 2022

Abstract
The role of the availability of calcium in limiting the breeding success and intensity of eggshell specking in birds remains unclear. Experimentally, we provided blue tits (Cyanistes caeruleus) and great tits (Parus major) in woodlands with underlying calcium-rich limestone or calcium-poor gritstone with calcium during the egg stage or during the entire reproductive period and examined their breeding success and eggshell speckling. When provided with calcium during the egg stage, experimental blue tits laid larger clutch sizes with higher clutch weights than controls, whilst experimental great tits had higher fledging success than controls. When provided with calcium throughout reproduction, there was no effect of treatment on blue tit reproductive success, but experimental great tits had higher hatching success and nestling masses than controls. Additional calcium during the egg stage resulted in experimental great tits, but not blue tits, laying less speckled eggs than controls, and additional calcium throughout reproduction led to experimental blue tits and great tits laying less speckled eggs than controls. The provision of calcium led to both species generally having higher levels of reproductive success and less speckled eggs than controls, irrespective of habitat geology, meaning that calcium availability does determine avian breeding success and eggshell specking.
Non-invasive oocyte quality assessment
Authors: Sciorio Romualdo , Miranian Daniel , Smith Gary D 
Published: February 2022

Abstract
Oocyte quality is perhaps the most important limiting factor in female fertility; however, the current methods of determining oocyte competence are only marginally capable of predicting a successful pregnancy. We aim to review the predictive value of non-invasive techniques for the assessment of human oocytes and their related cells and biofluids that pertain to their developmental competence. Investigation of the proteome, transcriptome, and hormonal makeup of follicular fluid, as well as cumulus-oocyte complexes are currently underway; however, prospective randomized non-selection-controlled trials of the future are needed before determining their prognostic value. The biological significance of polar body morphology and genetics are still unknown and the subject of debate. The predictive utility of zygotic viscoelasticity for embryo development has been demonstrated, but similar studies performed on oocytes have yet to be conducted. Metabolic profiling of culture media using human oocytes are also limited and may require integration of automated, high-throughput targeted metabolomic assessments in real time with microfluidic platforms. Light exposure to oocytes can be detrimental to subsequent development and utilization of time-lapse imaging and morphometrics of oocytes is wanting. Polarized light, Raman microspectroscopy, and coherent anti-Stokes Raman scattering are a few novel imaging tools that may play a more important role in future oocyte assessment. Ultimately, the integration of chemistry, genomics, microfluidics, microscopy, physics, and other biomedical engineering technologies into the basic studies of oocyte biology, and in testing and perfecting practical solutions of oocyte evaluation, are the future for non-invasive assessment of oocytes.
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation
Authors: Gambarini Victor , Pantos Olga , Kingsbury Joanne M , Weaver Louise , Handley Kim M , Lear Gavin 
Published: February 2022

Abstract
The number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data and the development of tools to facilitate their analysis. We developed the PlasticDB web application to address this need, which comprises a database of microorganisms and proteins reported to biodegrade plastics. Associated metadata, such as the techniques utilized to assess biodegradation, the environmental source of microbial isolate and presumed thermophilic traits are also reported. Proteins in the database are categorized according to the plastic type they are reported to degrade. Each protein structure has been predicted in silico and can be visualized or downloaded for further investigation. In addition to standard database functionalities, such as searching, filtering and retrieving database records, we implemented several analytical tools that accept inputs, including gene, genome, metagenome, transcriptomes, metatranscriptomes and taxa table data. Users can now analyze their datasets for the presence of putative plastic-degrading species and potential plastic-degrading proteins and pathways from those species.
Database URL:http://plasticdb.org.
Left atrial reservoir strain may be a load independent index of diastolic dysfunction in liver cirrhosis patients
Authors: Dimitroglou Y , Aggeli C , Alexopoulou A , Alexopoulos T , Patsourakos D , Polytarchou K , Kakiouzi V , Tsartsalis D , Valatsou A , Kastellanos S , Raftopoulos L , Angelis A , Mani I , Tousoulis D , Tsioufis K 
Published: February 2022

Abstract

Funding Acknowledgements
Type of funding sources: None.

Introduction
Cirrhotic cardiomyopathy is characterized by high cardiac output, reduced peripheral resistance and diastolic dysfunction. Specifically, diastolic dysfunction has been correlated with the prognosis in liver cirrhotis patients independently of the disease severity. Left atrial reservoir strain (LASr) is a novel index which is inversely correlated with left ventricular end-diastolic pressure, but has not been adequately studied in cirrhotic patients.

Purpose
To investigate the correlations between LASr and diastolic function or disease severity in cirrhotic patients.

Methods
Echocardiographic analysis of 51 consecutive cirrhotic patients was performed and images were analyzed off-line. LASr was calculated semi-automatically using dedicated software and was feasible in 49 patients. Clinical and biochemical examination was used to assess severity of liver disease by calculating MELD-Na score.

Results
Mean age was 58.0± 8.6 years, 37 (75.5%) were males, mean MELD-Na score was 15.6 ±7.5 and mean LASr was 39.7 ±12.5. LASr correlated with age (r=-0.415, p = 0.003), LAVI (r=-0.329, p = 0.022), e’ (r = 0.476, p = 0.001), E/e (r=-0.401, p = 0.004) and GLS (r=-0.388, p = 0.006), but not with ejection fraction, stroke volume or MELD-Na score. MELD-Na score correlated with ejection fraction (r = 0.316, p = 0.029), stroke volume (r = 0.549, p &lt; 0.001), left atrial volume index (r = 0.575, p &lt; 0.001), GLS (r = 0.521, p &lt; 0.001), right atrial end systolic area (r = 0.368, p = 0.011) and right ventricular diameter (r = 0.541, p &lt; 0.001) reflecting high cardiac output state in patients with advanced cirrhosis. LASr was significantly lower in patients with E/e’ &gt;14 (22.5 ± 13.6) when compared to patients with E/e’ 8-14 (37.3± 10.6, p = 0.039) and E/e’&lt;8 (44.7± 12.0, p = 0.003). The two latter groups also differed significantly (p = 0.034). LASr correlation with E/e’ was the only statistically significant correlation in a multiple regression model including left ventricular end diastolic volume, ejection fraction and left atrial volume (B=-1.371, P = 0.023). Correlation of LASr with MELD-Na score remained non-significant.

Conclusion
LASr correlates inversely with E/e’ ratio in liver cirrhotic patients, but does not correlate with load dependent echocardiographic parameters and disease severity. Hence in this special population, LASr may be an earlier and more specific index of diastolic dysfunction than traditional echocardiographic indices. Further studies are needed to examine the prognostic significance of LASr in cirrhotic patients.