bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning classification for D0 meson signal extraction in d+Au collisions
Authors: Bielčík J. , Hladká K. , Kramárik L. , Kůs V.
Published: February 2022

In heavy-ion collisions at large particle colliders, such as
LHC or RHIC, heavy-flavour (charm and beauty) quarks are produced
mainly through initial hard scatterings. Therefore, they can serve
as the probes of properties of the hot medium created in such
collisions. Additionally, in small collision systems, such as
d/p+Au collisions, cold nuclear matter effects can also affect the
charm quark production with respect to p+p collisions.

Hadrons, that contain heavy-flavour quarks, could not be directly
detected, thus they are measured via reconstruction of their decay
products. However, due to a large number of particles produced in
such collisions, separation of the decay products from combinatorial
background is challenging and advanced statistical analysis is
needed.

In this article, we exploit
D0 (D0)→K-
π+ (K+ π-) decay in order to investigate
performance of several machine learning algorithms with different
implementation approaches to find the most effective way how to
separate signal from random combinatorial background. For this
study, we use HIJING and STAR detector simulation of d+Au collisions
at √(sNN)=200 GeV embedded to the collisions recorded with the
STAR. In this paper we compare deep neural network implemented
using Keras with TensorFlow backend, random forest model implemented
using scikit-learn and boosted decision trees implemented by means
of the Toolkit for Multivariate Data Analysis with ROOT. Described
methods might be applied on reconstruction of any two-body decay in
high-energy physics experiments.
Nowcasting tracks of severe convective storms in West Africa from observations of land surface state
Authors: Taylor Christopher M , Klein Cornelia , Dione Cheikh , Parker Douglas J , Marsham John , Abdoulahat Diop Cheikh , Fletcher Jennifer , Saidou Chaibou Abdoul Aziz , Nafissa Dignon Bertin , Semeena Valiyaveetil Shamsudheen , Cole Steven J , Anderson Seonaid R
Published: February 2022

In tropical convective climates, where numerical weather prediction of rainfall has high uncertainty, nowcasting provides essential alerts of extreme events several hours ahead. In principle, short-term prediction of intense convective storms could benefit from knowledge of the slowly evolving land surface state in regions where soil moisture controls surface fluxes. Here we explore how near-real time (NRT) satellite observations of the land surface and convective clouds can be combined to aid early warning of severe weather in the Sahel on time scales of up to 12 h. Using land surface temperature (LST) as a proxy for soil moisture deficit, we characterise the state of the surface energy balance in NRT. We identify the most convectively active parts of mesoscale convective systems (MCSs) from spatial filtering of cloud-top temperature imagery. We find that predictive skill provided by LST data is maximised early in the rainy season, when soils are drier and vegetation less developed. Land-based skill in predicting intense convection extends well beyond the afternoon, with strong positive correlations between daytime LST and MCS activity persisting as far as the following morning in more arid conditions. For a Forecasting Testbed event during September 2021, we developed a simple technique to translate LST data into NRT maps quantifying the likelihood of convection based solely on land state. We used these maps in combination with convective features to nowcast the tracks of existing MCSs, and predict likely new initiation locations. This is the first time to our knowledge that nowcasting tools based principally on land observations have been developed. The strong sensitivity of Sahelian MCSs to soil moisture, in combination with MCS life times of typically 6–18 h, opens up the opportunity for nowcasting of hazardous weather well beyond what is possible from atmospheric observations alone, and could be applied elsewhere in the semi-arid tropics.
An investigation on the precipitates in T5 treated high vacuum die-casting AE44–2 magnesium alloy
Authors: Li Yongfeng , Wang Jinhui , Ma Hongbin , Zhen Zisheng , Liu Yanzhuo , Zhang Honggang , Jin Peipeng
Published: February 2022

The AE44-2 magnesium alloy was fabricated via die-casting under high vacuum (denoted as HVDC-AE44-2 alloy). The microstructures and mechanical properties of the aged HVDC-AE44-2 alloys were investigated. It was found that age strengthening can be achieved in the HVDC-AE44-2 alloys.The hardness, the yield strengths (YS) and the ultimate tensile strengths (UTS) of the HVDC-AE44-2 alloys after aging at 200 °C for 12 h (T5) increased by 8.8 HV, 30.5 MPa and 22.6 MPa, respectively, while the the elongations remained almost at the same level (The elongation was 19.6% in the die casting. The elongation was 19.1% in aged at 200 ℃ for 12h). It was also found that the improved age hardening ability was closely related to the Al4Mn and Al11Mn4 precipitation during aging. Both the α-Mg and the Al11RE3 have crystallographic orientation relationships with the Al4Mn. The slipping of dislocations was impeded by the precipitates during tensile deformation at room temperature, and the 〈a〉 dislocations were accumulated around the precipitates, which is the reason for the increase of the HVDC-AE44-2 alloy strength.
Hot corrosion behaviour of constant and pulsed current welded Hastelloy X in Na2SO4, V2O5, and NaCl salt mixture at 900 °C
Authors: Sathishkumar M , Manikandan M , Arivazhagan N , Arulmurugan B , Kumaran Selvaraj Senthil , Vignesh M , Rajakumar S , Rajkumar S
Published: February 2022

The high-temperature corrosion behavior of constant current gas tungsten arc (GTA) and pulsed current gas tungsten arc (PCGTA) welded Hastelloy X with different filler wires (C263 and ERNiCr-3) are studied for 50 cycles at 900 °C. Molten salt I (MS I) (75% Na2SO4 + 25% V2O5) and molten salt II (MS II) (75% Na2SO4 + 20% V2O5 + 5% NaCl) were coated on the welded specimens. MS II coated substrate shows the highest weight gain than MS I with a parabolic constant for GTA ERNiCr-3 as 21.440 × 10–6 mg2/(cm4.s). Whereas PCGTA C263 welded sample with MS I, revealed parabolic constant (lowest) of 0.008 × 10–6 mg2/ (cm4.s). Based on the results, an increasing pattern of hot corrosion resistance of substrates is arranged as GTA ERNiCr-3 < GTA C263 < PCGTA C263 < PCGTA ERNiCr-3. PCGTA shows more refined grains, higher grain boundary volume, better corrosion resistance, and more protective phases like Cr2O3, NiO, NiCr2O4, CoCr2O4, Al2O3, NiFe2O4, NbO than GTA weldment. But phases such as Fe2O3, MoO3, and Cr2S3 (non-protective phases) decrease corrosion resistance due to acid fluxing of alloying elements that promote the oxide scale exfoliation, spallation, chipping, and cracking. This study observed that PCGTA with C263 filler in MS I and MS II environment provides good corrosion resistance at high temperatures.
Leaf-level chlorophyll fluorescence and reflectance spectra of high latitude plants
Authors: Huemmrich K Fred , Campbell Petya , Vargas Z Sergio A , Sackett Sarah , Unger Steven , May Jeremy , Tweedie Craig , Middleton Elizabeth
Published: February 2022

Little is known about the chlorophyll fluorescence spectra for high latitude plants. A FluoWat leaf clip was used to measure leaf-level reflectance and chlorophyll fluorescence spectra of leaves of common high latitude plants to examine general spectral characteristics of these species. Fluorescence yield (Fyield) was calculated as the ratio of the emitted fluorescence divided by the absorbed radiation for the wavelengths from 400 nm up to the wavelength of the cut-off for the FluoWat low pass filter (either 650 or 700 nm). The Fyield spectra grouped into distinctly different patterns among different plant functional types. Black spruce (Picea mariana) Fyield spectra had little red fluorescence, which was reabsorbed in the shoot, but displayed a distinct far-red peak. Quaking aspen (Populus tremuloides) had both high red and far-red Fyield peaks, as did sweet coltsfoot (Petasites frigidus). Cotton grass (Eriophorum spp.) had both red and far-red Fyield peaks, but these peaks were much lower than for aspen or coltsfoot. Sphagnum moss (Sphagnum spp.) had a distinct Fyield red peak but low far-red fluorescence. Reindeer moss lichen (Cladonia rangiferina) had very low fluorescence levels, although when damp displayed a small red Fyield peak. These high latitude vegetation samples showed wide variations in Fyield spectral shapes. The Fyield values for the individual red or far-red peaks were poorly correlated to chlorophyll content, however the ratio of far-red to red Fyield showed a strong correlation with chlorophyll content. The spectral variability of these plants may provide information for remote sensing of vegetation type but may also confound attempts to measure high latitude vegetation biophysical characteristics and function using solar induced fluorescence (SIF).
Norm one Tori and Hasse norm principle
Authors: Hoshi Akinari , Kanai Kazuki , Yamasaki Aiichi
Published: February 2022

Let

k
k

be a field and

T
T

be an algebraic

k
k

-torus. In 1969, over a global field

k
k

, Voskresenskiǐ proved that there exists an exact sequence
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="0 right-arrow upper A left-parenthesis upper T right-parenthesis right-arrow upper H Superscript 1 Baseline left-parenthesis k comma upper P i c upper X overbar right-parenthesis Superscript logical-or Baseline right-arrow Ш left-parenthesis upper T right-parenthesis right-arrow 0">

0
→
A
(
T
)
→

H
1

(
k
,
Pic
⁡

X
¯

)
∨

→

Ш

(
T
)
→
0

0\to A(T)\to H^1(k,\operatorname {Pic}\overline {X})^\vee \to \Sha (T)\to 0

where

A
(
T
)

A(T)

is the kernel of the weak approximation of

T
T

,

Ш

(
T
)

\Sha (T)

is the Shafarevich-Tate group of

T
T

,

X
X

is a smooth

k
k

-compactification of

T
T

,

X
¯

=
X

×
k

k
¯

\overline {X}=X\times _k\overline {k}

,

Pic
⁡

X
¯

\operatorname {Pic}\overline {X}

is the Picard group of

X
¯

\overline {X}

and

∨
\vee

stands for the Pontryagin dual. On the other hand, in 1963, Ono proved that for the norm one torus

T
=

R

K

/

k

(
1
)

(

G

m

)

T=R^{(1)}_{K/k}(\mathbb {G}_m)

of

K

/

k

K/k

,

Ш

(
T
)
=
0

\Sha (T)=0

if and only if the Hasse norm principle holds for

K

/

k

K/k

. First, we determine

H
1

(
k
,
Pic
⁡

X
¯

)

H^1(k,\operatorname {Pic} \overline {X})

for algebraic

k
k

-tori

T
T

up to dimension

5
5

. Second, we determine

H
1

(
k
,
Pic
⁡

X
¯

)

H^1(k,\operatorname {Pic} \overline {X})

for norm one tori

T
=

R

K

/

k

(
1
)

(

G

m

)

T=R^{(1)}_{K/k}(\mathbb {G}_m)

with

[
K
:
k
]
=
n
≤
15

[K:k]=n\leq 15

and

n
≠
12

n\neq 12

. We also show that

H
1

(
k
,
Pic
⁡

X
¯

)
=
0

H^1(k,\operatorname {Pic} \overline {X})=0

for

T
=

R

K

/

k

(
1
)

(

G

m

)

T=R^{(1)}_{K/k}(\mathbb {G}_m)

when the Galois group of the Galois closure of

K

/

k

K/k

is the Mathieu group

M
n

≤

S
n

M_n\leq S_n

with

n
=
11
,
12
,
22
,
23
,
24

n=11,12,22,23,24

. Third, we give a necessary and sufficient condition for the Hasse norm principle for

K

/

k

K/k

with

[
K
:
k
]
=
n
≤
15

[K:k]=n\leq 15

and

n
≠
12

n\neq 12

. As applications of the results, we get the group

T
(
k
)

/

R

T(k)/R

of

R
R

-equivalence classes over a local field

k
k

via Colliot-Thélène and Sansuc’s formula and the Tamagawa number

τ
(
T
)

\tau (T)

over a number field

k
k

via Ono’s formula
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="tau left-parenthesis upper T right-parenthesis equals StartAbsoluteValue upper H Superscript 1 Baseline left-parenthesis k comma ModifyingAbove upper T With caret right-parenthesis EndAbsoluteValue slash StartAbsoluteValue Ш left-parenthesis upper T right-parenthesis EndAbsoluteValue">

τ
(
T
)
=

|

H
1

(
k
,

T
^

)

|

/

|

Ш

(
T
)

|

\tau (T)=|H^1(k,\widehat {T})|/|\Sha (T)|

.
Full discretization error analysis of exponential integrators for semilinear wave equations
Authors: Dörich Benjamin , Leibold Jan
Published: February 2022

In this article we prove full discretization error bounds for semilinear second-order evolution equations. We consider exponential integrators in time applied to an abstract nonconforming semidiscretization in space. Since the fully discrete schemes involve the spatially discretized semigroup, a crucial point in the error analysis is to eliminate the continuous semigroup in the representation of the exact solution. Hence, we derive a modified variation-of-constants formula driven by the spatially discretized semigroup which holds up to a discretization error. Our main results provide bounds for the full discretization errors for exponential Adams and explicit exponential Runge–Kutta methods. We show convergence with the stiff order of the corresponding exponential integrator in time, and errors stemming from the spatial discretization.

As an application of the abstract theory, we consider an acoustic wave equation with kinetic boundary conditions, for which we also present some numerical experiments to illustrate our results.
Liouville property of strongly transitive actions
Authors: Juschenko Kate
Published: February 2022

Liouville property of actions of discrete groups can be reformulated in terms of existence of co-Følner sets. Since every action of amenable group is Liouville, the property can be used for proving non-amenability. There are many groups that are defined by strongly transitive actions. In some cases amenability of such groups is an open problem. We define

n
n

-Liouville property of action to be Liouville property of point-wise action of the group on the sets of cardinality

n
n

. We reformulate

n
n

-Liouville property in terms of additive combinatorics and prove it for

n
=
1
,
2

n=1, 2

. The case

n
≥
3

n\geq 3

remains open.
The COVID-19 pandemic has highlighted the need to invest in care home research infrastructure
Authors: Gordon Adam L , Rick Caroline , Juszczak Ed , Montgomery Alan , Howard Rob , Guthrie Bruce , Lim Wei Shen , Shenkin Susan , Leighton Paul , Bath Philip M ,   the PROTECT-CH Triallists, Jonathan Ball , Matthew Glover , Jonathan Hewitt , Thomas Jaki , Dan Lasserson , Pip Logan , Philip Quinlan , Val Tate
Published: February 2022

The COVID-19 pandemic resulted in catastrophic levels of morbidity and mortality for care home residents. Despite this, research platforms for COVID-19 in care homes arrived late in the pandemic compared with other care settings. The Prophylactic Therapy in Care Homes Trial (PROTECT-CH) was established to provide a platform to deliver multi-centre cluster-randomized clinical trials of investigational medicinal products for COVID-19 prophylaxis in UK care homes. Commencing set-up in January 2021, this involved the design and development of novel infrastructure for contracting and recruitment, remote consent, staff training, research insurance, eligibility screening, prescribing, dispensing and adverse event reporting; such infrastructure being previously absent. By the time this infrastructure was in place, the widespread uptake of vaccination in care homes had changed the epidemiology of COVID-19 rendering the trial unfeasible. While some of the resources developed through PROTECT-CH will enable the future establishment of care home platform research, the near absence of care home trial infrastructure and nationally linked databases involving the care home sector will continue to significantly hamper progress. These issues are replicated in most other countries. Beyond COVID-19, there are many other research questions that require addressing to provide better care to people living in care homes. PROTECT-CH has exposed a clear need for research funders to invest in, and legislate for, an effective care home research infrastructure as part of national pandemic preparedness planning. Doing so would also invigorate care home research in the interim, leading to improved healthcare delivery specific to those living in this sector.
Pharmacists’ impact on quality and financial metrics utilizing virtual care platforms during the coronavirus pandemic
Authors: Glovacz Joseph W , Betts Sarah G , Cross Steven , Powell Justin
Published: February 2022

Purpose

Because of rising concern about coronavirus disease 2019 transmission, there has been a large shift from face-to-face, in-office visits to a virtual care model. The purpose of this article is to explain how Ascension Florida Gulf Coast was able to maximize the utility of ambulatory care pharmacists (ACPs) in the primary care setting during the pandemic and to provide guidance for creating a sustainable billing and practice model in the event of another global health crisis.

By employing telehealth services, our ACPs were able to continue to co-manage chronic disease states for documented diagnoses while still maintaining health-system revenue in the midst of a global health crisis. Utilizing various virtual platforms, ACPs were able to accommodate the needs of our patients while addressing concerns related to the compatibility and user friendliness of the platforms for our diverse patient population. ACPs used traditional incident-to evaluation and management services current procedural terminology billing codes with a virtual visit modifier for billing and tracking purposes.

Conclusion

Utilizing various virtual care platforms, our ACPs completed 447 patient encounters within the first 7 months of the pandemic. During this time, our ACPs addressed various population health metrics, specifically for patients diagnosed with diabetes without an active claim for a cholesterol-lowering medication, in addition to performing chronic disease management. Our ACPs had a 23% success rate for statin initiation in patients reviewed and contacted. By adopting virtual care options, our ACPs were able to effectively co-manage and educate patients while improving quality metrics and generating $50,662.24 in billable encounters for the health system during a global health crisis. The addition of ACP virtual encounters to primary care clinics both increases access to healthcare and improves patient care quality and outcomes while limiting revenue losses in our local health system.
Real-world evaluation of insulin requirements after GLP1 agonist or SGLT2 inhibitor initiation and titration
Authors: George Jamie , Lobkovich Alison , Nardolillo Joseph , Farhat Nada , Kolander Sarah , Thomas Emily
Published: February 2022

Purpose

To describe insulin adjustments made following initiation of glucagon-like peptide 1 agonist (GLP1a) or sodium-glucose cotransporter-2 inhibitor (SGLT2i) therapy in patients within a primary care setting.

Methods

This was a multicenter, retrospective cohort study conducted at an academic health system. Adults with type 2 diabetes mellitus initiated on a GLP1a or SGLT2i while on insulin and managed by an ambulatory care pharmacist were included. The primary endpoint was the percent change in total daily insulin dose at specified time points (2 weeks, 4 weeks, 6 weeks, 3 months, and 6 months) after agent initiation. The secondary endpoints included a glycosylated hemoglobin (HbA1c) value of less than 8%, change from baseline HbA1c, and safety profiles of GLP1a therapy and SGLT2i therapy.

Results

Of the 150 patients included, 123 were initiated on a GLP1a and 27 on an SGLT2i. After 6 months, GLP1a initiation had resulted in a mean 23.5% decrease (P < 0.001) in insulin dosage and SGLT2i resulted in a mean 0.2% increase (P = 0.20). Insulin dosage reduction with GLP1a use was significantly different between baseline and each time point (P < 0.001). About 72% of patients initiated on a GLP1a and 59% of those initiated on an SGLT2i achieved an HbA1c value of less than 8%. The mean absolute change from baseline in HbA1c concentration was –1.7% with GLP1a use and –1.5% with SGLT2i use (P < 0.001 for both comparisons with baseline values). Hypoglycemia occurred in 21% of patients on a GLP1a and 11% of those on an SGLT2i.

Conclusion

After GLP1a initiation, the mean total daily insulin dose decreased by 23.5%; after SGLT2i initiation, insulin requirements increased by a mean of 0.2%. These results will help guide insulin adjustments after initiation of these medications.
Comparison of the stability of CYP105A1 and its variants engineered for production of active forms of vitamin D
Authors: Takita Teisuke , Sakuma Hiro , Ohashi Ren , Nilouyal Somaye , Nemoto Sho , Wada Moeka , Yogo Yuya , Yasuda Kaori , Ikushiro Shinichi , Sakaki Toshiyuki , Yasukawa Kiyoshi
Published: February 2022

CYP105A1 from Streptomyces griseolus converts vitamin D3 to its biologically active form, 1α,25-dihydroxy vitamin D3. R73A/R84A mutation enhanced the 1α- and 25-hydroxylation activity for vitamin D3, while M239A mutation generated the 1α-hydroxylation activity for vitamin D2. In this study, the stability of six CYP105A1 enzymes, including 5 variants (R73A/R84A, M239A, R73A/R84A/M239A (=TriA), TriA/E90A, and TriA/E90D), was examined. Circular dichroism analysis revealed that M239A markedly reduces the enzyme stability. Protein fluorescence analysis disclosed that these mutations, especially M239A, induce large changes in the local conformation around Trp residues. Strong stabilizing effect of glycerol was observed. Nondenaturing PAGE analysis showed that CYP105A1 enzymes are prone to self-association. Fluorescence analysis using a hydrophobic probe 8-anilino-1-naphthalenesulfonic acid suggested that M239A mutation enhances self-association and that E90A and E90D mutations, in cooperation with M239A, accelerate self-association with little effect on the stability.
Bibliometric review of ATAC-Seq and its application in gene expression
Authors: Luo Liheng , Gribskov Michael , Wang Sufang
Published: February 2022

With recent advances in high-throughput next-generation sequencing, it is possible to describe the regulation and expression of genes at multiple levels. An assay for transposase-accessible chromatin using sequencing (ATAC-seq), which uses Tn5 transposase to sequence protein-free binding regions of the genome, can be combined with chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) and ribonucleic acid sequencing (RNA-seq) to provide a detailed description of gene expression. Here, we reviewed the literature on ATAC-seq and described the characteristics of ATAC-seq publications. We then briefly introduced the principles of RNA-seq, ChIP-seq and ATAC-seq, focusing on the main features of the techniques. We built a phylogenetic tree from species that had been previously studied by using ATAC-seq. Studies of Mus musculus and Homo sapiens account for approximately 90% of the total ATAC-seq data, while other species are still in the process of accumulating data. We summarized the findings from human diseases and other species, illustrating the cutting-edge discoveries and the role of multi-omics data analysis in current research. Moreover, we collected and compared ATAC-seq analysis pipelines, which allowed biological researchers who lack programming skills to better analyze and explore ATAC-seq data. Through this review, it is clear that multi-omics analysis and single-cell sequencing technology will become the mainstream approach in future research.
Research progress of miRNA–disease association prediction and comparison of related algorithms
Authors: Yu Liang , Zheng Yujia , Ju Bingyi , Ao Chunyan , Gao Lin
Published: February 2022

With an in-depth understanding of noncoding ribonucleic acid (RNA), many studies have shown that microRNA (miRNA) plays an important role in human diseases. Because traditional biological experiments are time-consuming and laborious, new calculation methods have recently been developed to predict associations between miRNA and diseases. In this review, we collected various miRNA–disease association prediction models proposed in recent years and used two common data sets to evaluate the performance of the prediction models. First, we systematically summarized the commonly used databases and similarity data for predicting miRNA–disease associations, and then divided the various calculation models into four categories for summary and detailed introduction. In this study, two independent datasets (D5430 and D6088) were compiled to systematically evaluate 11 publicly available prediction tools for miRNA–disease associations. The experimental results indicate that the methods based on information dissemination and the method based on scoring function require shorter running time. The method based on matrix transformation often requires a longer running time, but the overall prediction result is better than the previous two methods. We hope that the summary of work related to miRNA and disease will provide comprehensive knowledge for predicting the relationship between miRNA and disease and contribute to advanced computation tools in the future.
Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS
Authors: Irlmeier Rebecca , Hughey Jacob J , Bastarache Lisa , Denny Joshua C , Chen Qingxia
Published: February 2022

Motivation

Logistic regression models are used in genomic studies to analyze the genetic data linked to electronic health records (EHRs), and do not take full usage of the time-to-event information available in EHRs. Previous work has shown that Cox regression, which can account for left truncation and right censoring in EHRs, increased the power to detect genotype–phenotype associations compared to logistic regression. We extend this to evaluate the relative performance of Cox regression and various logistic regression models in the presence of positive errors in event time (delayed event time), relating to recorded event time accuracy.

Results

One Cox model and three logistic regression models were considered under different scenarios of delayed event time. Extensive simulations and a genomic study application were used to evaluate the impact of delayed event time. While logistic regression does not model the time-to-event directly, various logistic regression models used in the literature were more sensitive to delayed event time than Cox regression. Results highlighted the importance to identify and exclude the patients diagnosed before entry time. Cox regression had similar or modest improvement in statistical power over various logistic regression models at controlled type I error. This was supported by the empirical data, where the Cox models steadily had the highest sensitivity to detect known genotype–phenotype associations under all scenarios of delayed event time.

Availability and implementation

Access to individual-level EHR and genotype data is restricted by the IRB. Simulation code and R script for data process are at: https://github.com/QingxiaCindyChen/CoxRobustEHR.git

Supplementary information

Supplementary data are available at Bioinformatics online.
riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow
Authors: Cope Alexander L , Anderson Felicity , Favate John , Jackson Michael , Mok Amanda , Kurowska Anna , Liu Junchen , MacKenzie Emma , Shivakumar Vikram , Tilton Peter , Winterbourne Sophie M , Xue Siyin , Kavoussanakis Kostas , Lareau Liana F , Shah Premal , Wallace Edward W J
Published: February 2022

Motivation

Ribosome profiling, or Ribo-seq, is the state-of-the-art method for quantifying protein synthesis in living cells. Computational analysis of Ribo-seq data remains challenging due to the complexity of the procedure, as well as variations introduced for specific organisms or specialized analyses.

Results

We present riboviz 2, an updated riboviz package, for the comprehensive transcript-centric analysis and visualization of Ribo-seq data. riboviz 2 includes an analysis workflow built on the Nextflow workflow management system for end-to-end processing of Ribo-seq data. riboviz 2 has been extensively tested on diverse species and library preparation strategies, including multiplexed samples. riboviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses with the pipeline.

Availability and implementation

riboviz 2 is freely available at github.com/riboviz/riboviz.
Irx3 promotes gap junction communication between uterine stromal cells to regulate vascularization during embryo implantation
Authors: Brown Ryan M , Wang Linda , Fu Anqi , Kannan Athilakshmi , Mussar Michael , Bagchi Indrani C , Jorgensen Joan S
Published: February 2022

Appropriate embryo-uterine interactions are essential for implantation. Besides oocyte abnormalities, implantation failure is a major contributor to early pregnancy loss. Previously, we demonstrated that two members of the Iroquois homeobox transcription factor family, IRX3 and IRX5, exhibited distinct and dynamic expression profiles in the developing ovary to promote oocyte and follicle survival. Elimination of each gene independently caused subfertility, but with different breeding pattern outcomes. Irx3 KO (Irx3LacZ/LacZ) females produced fewer pups throughout their reproductive lifespan which could only be partially explained by poor oocyte quality. Thus, we hypothesized that IRX3 is also expressed in the uterus where it acts to support pregnancy. To test this hypothesis, we harvested pregnant uteri from control and Irx3 KO females to evaluate IRX3 expression profiles and the integrity of embryo implantation sites. Our results indicate that IRX3 is expressed in the endometrial stromal cells at day 4 of pregnancy (D4) with peak expression at D5–D6, and then greatly diminishes by D7. Further, studies showed that while embryos were able to attach to the uterus, implantation sites in Irx3 KO pregnant mice exhibited impaired vascularization and abnormal expression of decidualization markers. Finally, we also observed an impaired response of the Irx3 KO uteri to an artificial deciduogenic stimulus, indicating a critical role of this factor in regulating the decidualization program. Together, these data established that IRX3 promotes female fertility via at least two different mechanisms: (1) promoting competent oocytes and (2) facilitating functional embryo–uterine interactions during implantation.
Making the ‘Local’ Visible in Social Work Education: Insights from Nigeria and Scotland on (Re)balancing and Contextualising Indigenous and International Knowledge
Authors: Levy Susan , Okoye Uzoma O , Ingram Richard
Published: February 2022

Social work in the twenty-first century is maturing as a global profession. This comparative study offers an original contribution to the evolving discussion in the field of international social work. The paper makes visible the socio-spatial dimensions and contested interpretations of international and indigenous knowledge through the experiences of social work students in the Global South and Global North. Drawing on findings from an online survey completed by undergraduate and postgraduate Nigerian and Scottish social work students (n = 142), the paper provides insights into the students’ experiences, expectations and perceived challenges. The Nigerian students critiqued the international (Western) knowledge informing their learning and practice, questioned the absence of indigenous knowledge and were aware of the importance, and challenges, of working with cultural diversity. The Scottish students showed little criticality of the Western (local) knowledge underpinning their learning and practice, did not prioritise learning about international social work and highlighted tensions between working with a culture of neoliberalism and social work values and social justice. We call for raising awareness of the epistemological foundations of what is included/excluded in curriculum and why, making the ‘local’ visible through re-balancing and contextualising the use of international and indigenous knowledge within social work.
Lower Rates of Emergency Department Visits and Hospitalizations Among Patients With Chronic Hepatitis C With Sustained Virological Response to Interferon-Free Direct-Acting Antiviral Therapy (2014–2018)
Authors: Gordon Stuart C , Teshale Eyasu H , Spradling Philip R , Moorman Anne C , Boscarino Joseph A , Schmidt Mark A , Daida Yihe G , Rupp Loralee B , Trudeau Sheri , Zhang Jiaqi , Lu Mei ,   CHeCS Investigators, Teshale Eyasu H , Spradling Philip R , Moorman Anne C , Xing Jian , Zhong Yuna , Gordon Stuart C , Rupp Loralee B , Trudeau Sheri , Lu Mei , Li Jia , Akkerman Nonna , Zhou Yueren , Boscarino Joseph A , Daar Zahra S , Smith Robert E , Daida Yihe G , Trinacty Connie Mah , Lai Jonathan W , Nie Sixiang , Wong Carmen P , Schmidt Mark A , Donald Judy L
Published: February 2022

We compared rates of emergency department visits and hospitalizations between patients with hepatitis C virus who achieved sustained virological response after direct-acting antiviral therapy (case patients) and matched controls. Among 3049 pairs, case patients demonstrated lower rates of liver-related emergency department visits (P = .01) than controls; all-cause and liver-related hospitalization rates and number of hospitalized days were also lower in case patients (P < .001).
AmBisome Monotherapy and Combination AmBisome–Miltefosine Therapy for the Treatment of Visceral Leishmaniasis in Patients Coinfected With Human Immunodeficiency Virus in India: A Randomized Open-Label, Parallel-Arm, Phase 3 Trial
Authors: Burza Sakib , Mahajan Raman , Kazmi Shahwar , Alexander Neal , Kumar Deepak , Kumar Vikash , Lasry Estrella , Harshana Amit , de Lima Pereira Alan , Das Pradeep , Verma Neena , Das Vidya Nand Ravi , Lal Chandra Shekhar , Rewari Bharat , Goyal Vishal , Rijal Suman , Alves Fabiana , Gill Naresh , Pandey Krishna
Published: February 2022

Background

Visceral leishmaniasis (VL) in patients with human immunodeficiency virus (HIV) presents an increasingly important patient cohort in areas where both infections are endemic. Evidence for treatment is sparce, with no high-quality studies from the Indian subcontinent.

Methods

This is a randomized, open-label, parallel-arm, phase 3 trial conducted within a single hospital in Patna, India. One hundred and fifty patients aged ≥18 years with serologically confirmed HIV and parasitologically confirmed VL were randomly allocated to 1 of 2 treatment arms, either a total 40 mg/kg intravenous liposomal amphotericin B (AmBisome; Gilead Pharmaceuticals) administered in 8 equal doses over 24 days or a total 30 mg/kg intravenous AmBisome administered in 6 equal doses given concomitantly with a total 1.4 g oral miltefosine administered through 2 daily doses of 50 mg over 14 days. The primary outcome was intention-to-treat relapse-free survival at day 210, defined as absence of signs and symptoms of VL or, if symptomatic, negative parasitological investigations.

Results

Among 243 patients assessed for eligibility, 150 were recruited between 2 January 2017 and 5 April 2018, with no loss to follow-up. Relapse-free survival at day 210 was 85% (64/75; 95% CI, 77–100%) in the monotherapy arm, and 96%, (72/75; 90–100%) in the combination arm. Nineteen percent (28/150) were infected with concurrent tuberculosis, divided equally between arms. Excluding those with concurrent tuberculosis, relapse-free survival at day 210 was 90% (55/61; 82–100%) in the monotherapy and 97% (59/61; 91–100%) in the combination therapy arm. Serious adverse events were uncommon and similar in each arm.

Conclusions

Combination therapy appears to be safe, well tolerated, and effective, and halves treatment duration of current recommendations.

Clinical Trials Registration

Clinical Trial Registry India (CTRI/2015/05/005807; the protocol is available online at https://osf.io/avz7r).
Theory of Mind and Alexithymia in Deaf and Hard-of-Hearing Young Adults
Authors: Blose Brittany A , Schenkel Lindsay S
Published: February 2022

The aim of the current study was to examine theory of mind (ToM), the ability to infer the mental states of others, in young adults who are deaf and hard-of-hearing (DHH), and to explore the influence of alexithymia, an inability to understand emotions of the self and others, on ToM performance in this group. Compared to participants with typical hearing, DHH participants displayed significantly lower affective ToM skills and greater alexithymia. After accounting for verbal intelligence quotient, hearing status and alexithymia significantly contributed to poorer ToM performance, accounting for over 14% of the variance. Having a parent who is deaf and being part of the Deaf community were associated with better emotion processing and appear to be important protective factors. Findings provide support that ToM difficulties may linger into young adulthood among DHH individuals and that alexithymia may be a contributing factor. Early intervention programs emphasizing emotional understanding, perspective-taking, and communication skills are warranted for DHH children as well as their caregivers.
Suggested modification of the recommendations for echocardiography in patients with clinical suspicion of infective endocarditis
Authors: Damlin A , Eriksson MJE
Published: February 2022

Funding Acknowledgements

Type of funding sources: None.

Introduction

Infective endocarditis (IE) is a serious condition that requires prompt diagnosis and treatment. Transthoracic echocardiography (TTE) is usually the initial imaging modality, however transoesophageal echocardiography (TOE) is often necessary because of its higher sensitivity for IE compared with TTE. Yet, TOE has an increased risk of complications. The European Society of Cardiology (ESC) has established guidelines for the management of IE with recommendations for the use of TOE in patients with clinical suspicion of IE.

Purpose

This project aims to evaluate the ESC recommendations for the use of TOE in patients with clinical suspicion of IE. The purpose of the study is further to examine whether the ESC recommendations for TOE among patients with clinical suspicion of IE result in an unnecessarily large number of negative TOE examinations.

Methods

All TOE examinations performed due to referrals of patients with clinical suspicion of IE between 1 May 2019 and 30 April 2020 at a university hospital in our city were analysed. The variables included for analysis were age; sex; cardiac comorbidities; prosthetic valves; blood culture results; results from TTE and TOE; number of TOEs during the inclusion period; Duke criteria. The TOE and TTE results were compared in relation to the ESC guidelines.

Results

In total 195 TOE examinations from 160 patients were included, of which 61 (31%) TOEs were positive for IE. All examinations were of patients with clinical suspicion of IE, of which 37 (19%) had negative TTE. Of the 37 patients with negative TTE, 13 had prosthetic valve or intracardiac device of which 5 had positive TOE. All the 24 (12%) examinations with negative TTE and no prosthetic valve or intracardiac device had negative TOE.

Conclusions

The ESC recommendations for TOE in patients with clinical suspicion of IE are probably broad enough not to miss patients with IE, but there might be an unnecessarily large number of patients that get referred for TOE with negative results. To avoid this, we propose a modification of the recommendations for TOE in patients with clinical suspicion of IE. Negative TTE examination with good image quality and no indications for TOE according to Fig 1, could result in avoiding unnecessary TOE examinations without jeopardizing the IE diagnosis. Abstract Figure. Fig 1
Atrial mechanics in anthracycline chemotherapy: insights into a prospective study
Authors: Vahabi S , Kharati-Koopaei E , Norouzi M , Maddox J , Humphreys A , Hancock H , Zaman A , Austin D
Published: February 2022

Funding Acknowledgements

Type of funding sources: Public hospital(s). Main funding source(s): South Tees Research and Development Fund

Background

In cancer treatment, detection of anthracycline induced cardiotoxicity (AIC) has been dependent on serial cardiac imaging to identify a reduction in left ventricular ejection fraction (LVEF) and more recently LV global longitudinal strain (GLS). However, studies have failed to assess the adverse effects of these agents on other cardiac chambers such as the left (LA) and right atria (RA).

Purpose

The PROACT PLUS study is an observational, prospective, cohort study investigating the effects of anthracyclines on the left and right atrial mechanics using 2 dimensional speckle tracking echocardiography (STE). We hypothesize that anthracyclines can affect the heart as a whole rather than solely affecting the LV.

Methods

From October 2018 to March 2020, patients with a new diagnosis of lymphoma or breast cancer receiving anthracycline chemotherapy were recruited into this study. Echocardiography was performed pre-chemotherapy (V1) and 1 month post-chemotherapy (V2). LA and RA volumes, LA (4-chamber)- and RA GLS, reservoir strains (RS), conduit strains (CS), contractile strains (CoS), peak-systolic (PS) strain-rates, early-diastolic (ED) strain-rates, and late-diastolic (LD) strain-rates were measured offline using vendor-independent software. This study was ethically approved by the Health Research Association (REC reference 18/EM/0177).

Results

A total number of 62 patients were recruited into this study. Unfortunately, 7 patients passed away during their treatment and 5 failed to attend their follow-up appointment at V2. From V1 to V2, there was a significant deterioration in the LA CS (-18.1% vs. -14.5%, p = 0.02) and LA ED strain-rate (-1.24 1/s vs. -0.86 1/s, p = 0.001). There was no other statistical significant change in the LA volume or other strain parameters. Additionally, there was a statistically significant decline in RA GLS (34.9% vs. 30.8%, p = 0.029), RA RS (41.1% vs. 37.1%, p = 0.03), RA CS (-23.8 vs. -20.6, p = 0.05), and RA ED strain-rate (-1.17 vs. -0.99, p = 0.02) with no significant change in the RA volume and other measures of RA strain.

Conclusion

These findings support our hypothesis that anthracyclines exert their cardiotoxic effects on all cardiac chambers including the atria. Whether these changes lead to subsequent permanent structural abnormalities in the atria hence increasing the future risk of atrial arrhythmias, or whether these changes predate subsequent cardiac dysfunction and poor prognosis, remains unknown. Long-term follow up and assessment of atrial mechanics is crucial in better understanding of AIC to help guide the future monitoring and management of patients undergoing cancer treatment.
Automated left atrial strain after electrical cardioversion for atrial fibrillation
Authors: Orphanou N , Zamfir T , Siama A , Michelinakis N , Tsoukas A
Published: February 2022

Funding Acknowledgements

Type of funding sources: None.

Introduction

Evidence shows that atrial dysfunction and stunning occur, after successful cardioversion from persistent atrial fibrillation (AF) to sinus rhythm (SR). Electrical and mechanical recovery of the left atrium (LA), do not seem to coincide. Traditional Doppler parameters show reduced atrial contractility immediately after cardioversion, while mechanical improvement in atrial function mainly occurs within the first 4 weeks after sinus rhythm restoration.

Purpose

This study aimed to determine whether automated left atrial strain (auto-LA strain) could be used to measure global LA function and the time required for mechanical improvement to be seen in LA after cardioversion.

Methods

Auto-LA strain was measured via transthoracic echocardiography in 20 patients with persistent AF who had been cardioverted to SR and followed up for 3 months, and in a cohort of 20 healthy individuals. Conventional measures of atrial function derived from transmitral pulsed Doppler and tissue Doppler imaging of lateral mitral annulus were included, such as transmitral A wave velocity, A wave velocity-time integral, atrial fraction, A" wave velocity, and A" velocity-time integral.

Results

Immediately after cardioversion auto-LA strain was significantly lower than in control subjects. Atrial function improved over time with maximal change observed at 1 month after cardioversion. Doppler tissue imaging parameters were also normalised after 1 month of restoration to SR. Despite this initial improvement in LA function, the values of auto-LA strain remained stable for the following 3 months.

Conclusion

Although the electrical function of LA is immediately restored after successful cardioversion in AF patients, there remains a persistent degree of atrial dysfunction for at least 3 months. This difference could explain the increased propensity for these patients to develop recurrent atrial fibrillation. Additionally, this dysfunction could indicate longer-term use of anti-arrhythmic and antithrombotic medications in the AF cohort. Abstract Figure.
Association of COVID-19 with impaired endothelial glycocalyx, vascular function and myocardial efficiency four months after infection
Authors: Katogiannis K , Ikonomidis I , Thymis J , Mitrakou A , Kountouri A , Stamoulis K , Korakas E , Varlamos C , Andreadou I , Tsoumani M , Bamias A , Thomas K , Antoniadou A , Dimopoulos MA , Lambadiari V
Published: February 2022

Funding Acknowledgements

Type of funding sources: None.

Aims

SARS-CoV-2 infection may lead to endothelial and vascular dysfunction. We

investigated alterations of arterial stiffness, endothelial coronary and myocardial

function markers four months after COVID-19 infection.

Methods

In a case-control prospective study, we included 100 patients four months after COVID-19 infection, 50 age- and sex-matched healthy individuals. We measured a) pulse wave velocity (PWV), b) flow-mediated dilation (FMD) of brachial artery, c) coronary Flow Reserve (CFR) by Doppler echocardiography d) left ventricular (LV) global longitudinal strain (GLS), e) left ventricular myocardial work index, constructive work, wasted work and work efficiency and e) von-Willenbrand factor and thrombomodulin as endothelial biomarkers.

Results

COVID-19 patients had lower CFR and FMD values than controls (2.39 ± 0.39 vs 3.31 ± 0.59, p = 0.0122, 5.12 ± 2.95% vs 8.12 ± 2.23%, p = 0.006 respectively). Compared to controls, COVID-19 patients had higher PWV (PWVc-f 12.32 ± 2.44 vs 10.11 ± 1.85 m/sec, p = 0.033) and impaired LV GLS (-19.11 ± 2.14% vs -20.41 ± 1.61%, p = 0.001). Compared to controls, COVID-19 patients had higher myocardial work index, and wasted work (2067.7 ± 325.9 mmHg% vs 1929.4 ± 312.7 mmHg%, p = 0.026, 104.6 ± 58.9 mmHg% vs 75.1 ± 52.6 mmHg%, p = 0.008, respectively), while myocardial efficiency was lower (94.8 ± 2.5% vs 96.06 ± 2.3%, p = 0.008). and thrombomodulin were higher in COVID-19 patients than controls (3716.63 ± 188.36 vs 2590.02 ± 156.51pg/ml, p < 0.001). MDA was higher in COVID-19 patients than controls (10.55 ± 2.45 vs 1.01 ± 0.50 nmole/L, p = 0.001). Residual cardiovascular symptoms at 4 months were associated with oxidative stress markers. Myocardial work efficiency was related with PWV (F=-0.309, p = 0.016) and vWillenbrand (F=-0.541, p = 0.037). Myocardial wasted work was related with PWV (F = 0.255, p = 0.047) and vWillenbrand (F = 0.610, p = 0.016).

Conclusions

SARS-CoV-2 may cause vascular dysfunction, followed by a waste of cardiac work, in order to compensate for increased arterial stiffness 4 months after infection.