bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Use and Promise of Conversational Agents in Digital Health
Authors: Dingler Tilman , Kwasnicka Dominika , Wei Jing , Gong Enying , Oldenburg Brian 
Published: September 2021

Summary
Objectives: To describe the use and promise of conversational agents in digital health—including health promotion andprevention—and how they can be combined with other new technologies to provide healthcare at home.
Method: A narrative review of recent advances in technologies underpinning conversational agents and their use and potential for healthcare and improving health outcomes.
Results: By responding to written and spoken language, conversational agents present a versatile, natural user interface and have the potential to make their services and applications more widely accessible. Historically, conversational interfaces for health applications have focused mainly on mental health, but with an increase in affordable devices and the modernization of health services, conversational agents are becoming more widely deployed across the health system. We present our work on context-aware voice assistants capable of proactively engaging users and delivering health information and services. The proactive voice agents we deploy, allow us to conduct experience sampling in people's homes and to collect information about the contexts in which users are interacting with them.
Conclusion: In this article, we describe the state-of-the-art of these and other enabling technologies for speech and conversation and discuss ongoing research efforts to develop conversational agents that “live” with patients and customize their service offerings around their needs. These agents can function as ‘digital companions’ who will send reminders about medications and appointments, proactively check in to gather self-assessments, and follow up with patients on their treatment plans. Together with an unobtrusive and continuous collection of other health data, conversational agents can provide novel and deeply personalized access to digital health care, and they will continue to become an increasingly important part of the ecosystem for future healthcare delivery.
Health Data, Information, and Knowledge Sharing for Addressing the COVID-19
Authors: Soualmia Lina F. , Hollis Kate Fultz , Mougin Fleur , Séroussi Brigitte 
Published: September 2021

Summary
Objectives: To introduce the 2021 International Medical Informatics Association (IMIA) Yearbook by the editors.
Methods: The editorial provides an introduction and overview to the 2021 IMIA Yearbook whose special topic is “Managing Pandemics with Health Informatics - Successes and Challenges”. The Special Topic, the keynote paper, and survey papers are discussed. The IMIA President's statement and the IMIA dialogue with the World Health Organization are introduced. The sections’ changes in the Yearbook Editorial Committee are also described.
Results: Health informatics, in the context of a global pandemic, led to the development of ways to collect, standardize, disseminate and reuse data worldwide: public health data but also information from social networks and scientific literature. Fact checking methods were mostly based on artificial intelligence and natural language processing. The pandemic also introduced new challenges for telehealth support in times of critical response. Next generation sequencing in bioinformatics helped in decoding the sequence of the virus and the development of messenger ribonucleic acid (mRNA) vaccines.
Conclusions: The Corona Virus Disease 2019 (COVID-19) pandemic shows the need for timely, reliable, open, and globally available information to support decision making and efficiently control outbreaks. Applying Findable, Accessible, Interoperable, and Reusable (FAIR) requirements for data is a key success factor while challenging ethical issues have to be considered.
Teaching and Training Surgeons in Robotic Colorectal Surgery
Authors: Soliman Mark K. , Tammany Alison J. 
Published: September 2021

AbstractRobotic surgery is becoming more popular among practicing physicians as a new modality with improved visualization and mobility (1–2). As patients also desire minimally invasive procedures with quicker recoveries, there is a desire for new surgical residents and fellows to pursue robotic techniques in training (3–4). To develop a new colorectal robotics training program, an institution needs a well-formulated plan for the trainees and mentors with realistic expectations. The development of a robotics training program has potential obstacles, including increased initial cost, longer operative times, and overcoming learning curves. We have devised a four-phase training protocol for residents in colorectal surgical fellowship. Each of these phases attempts to create a curricular framework that outlines logical progression and sets expectations for trainees, Program Directors, and residency faculty. Phase zero begins prior to fellowship and is preparatory. Phase one focuses on an introduction to robotics with learning bedside console troubleshooting and simulation exercises. Phase Two prioritizes operative experience and safety while completing steps independently in a progressive fashion. Phase Three polishes the resident prior to graduation for future practice. We recommend frequent evaluation and open-mindedness while establishing a focused robotics program. The end goal is to graduate fellows with an equivalency certificate who can continue to practice colorectal robotic surgery.
Immunotherapy in Patients with Lung Cancer with Driver Mutations: A Single-Centre Experience
Authors: Rauthan Amit , Patil Poonam , Aswath Rajashree , Yashas Nitin , Ningade Gaurav 
Published: September 2021

Abstract
Introduction Immunotherapy has revolutionized treatment in metastatic nonsmall cell lung cancer (NSCLC) without driver mutations. Trial data shows that programmed death-1/PDL1 blockade in epidermal growth factor receptor (EGFR) and other driver mutation positive lung cancers is not beneficial; and instead maybe detrimental. Here, we evaluated the efficacy of immune check point inhibitors in a series of patients with EGFR and other driver mutation–positive advanced NSCLC.
Objectives This study was aimed to evaluate the efficacy of immune check point inhibitors in a series of patients with EGFR and other driver mutation–positive advanced NSCLC.
Materials and Methods We retrospectively analyzed 75 patients which received PD1/PDL1 inhibitors for advanced NSCL between January 2017 and January 2020. Ten patients were detected to have driver mutations on either tumor tissue or blood by next-generation sequencing (NGS). PDL1 status was assessed on SP263 ventana platform.
Results Out of 10 patients, 7 were male and 3 were female. EGFR was detected in six patients (three on tumor and three in blood NGS), MET exon 14 skipping mutation in two patients, and RAS mutation in two patients on NGS in blood. Immunotherapy combined with chemotherapy was given in 5 (50%) patients, immunotherapy + bevacizumab + chemotherapy in two (20%) and immunotherapy alone in three patients (30%). Immunotherapy was started as first line in four patients as tumor tissue was negative for EGFR, ALK, and ROS1 by single gene testing. The remaining six patients received immunotherapy on progression in the second or subsequent lines. On NGS testing at progression, EGFR mutation was detected in one patient, MET exon 14 skip mutation was detected in two patients, and RAS mutation was detected in two patients. Immunotherapy alone was used in three patients in view of advanced age and multiple comorbidities. The median progression-free survival (PFS) was 5 months (range: 2–11 months). Two patients who received chemotherapy + bevacizumab + immunotherapy continue to do well without progression at 9 months.
Conclusion PD1/PDL1 checkpoint inhibitors seem to have a limited impact in treatment in patients with driver mutations. Molecular testing by NGS is recommended either on tumor tissue or on blood by NGS if single gene testing for EGFR/ALK/ROS1 alterations is negative. We recommend not using single agent checkpoint inhibitors in molecular driven advanced NSCLC even with high PDL1 expression. We do see benefit in patients who received PD1/PDL1 inhibitors in combination with chemotherapy with bevacizumab. In conclusion, in patients with molecular-driven NSCLC who progress after standard therapy can be treated with PD1/PDL1 inhibitors, but this should always be given in combination with chemotherapy and bevacizumab.
Weekly Etoposide and Platinum in Small-Cell Lung Cancer: Hope and Scope for Fragile Patients
Authors: Sundriyal Deepak , Kumar Parmod , Gogisetti Yeswanth , Sehrawat Amit 
Published: September 2021

Abstract
Introduction Small-cell lung cancer (SCLC) is an aggressive and chemo-sensitive disease. Many patients present in an advanced stage and with a poor performance status (PS). In such a condition, the treatment dilemma due to poor condition advocates alternative treatment approach rather than standard chemotherapy. One way of usual practice is to split the chemotherapy into a weekly schedule. However, there is limited data regarding the actual benefit of weekly chemotherapy. We hypothesize that a weekly chemotherapy with etoposide/platinum combination will be feasible and safe in patients of advanced-stage SCLC with poor PS.
Objectives This study was aimed to determine whether weekly etoposide/platinum chemotherapy is a safe option for patients with advanced stage, poor PS, and SCLC who are otherwise unfit for systemic anticancer therapy.
Materials and Methods We retrospectively analyzed the data of SCLC patients presented to our center from July 2018 to September 2020. We analyzed that treatment, survival, and clinical benefit data. We also analyzed the benefit of weekly etoposide/platinum in otherwise unfit for chemotherapy.
Results One hundred and fifty patients of lung cancer presente to our department between July 2018 and September 2020; SCLC constituted 34% (53 cases). In SCLC patients, the median overall survival was 2.5 months. Fourteen (26%) patients with SCLC were unable to start any oncological intervention. Ten (19%) patients could receive only one cycle of standard 3 weekly chemotherapy. Five patients with an advanced-stage SCLC and an ECOG-PS of 4, otherwise unfit for any systemic anticancer therapy, were started on weekly chemotherapy with etoposide (60–80 mg/m2) and carboplatin (AUC 2). Four patients demonstrated a partial response (PR) while one demonstrated stable disease (SD) after 9 weeks of therapy. Improvement in PS was noted in all patients. Median progression-free survival (PFS) and overall survival (OS) were 137 and 164 days, respectively. Two patients died of disease progression, one died of massive pulmonary embolism, while two were alive and continuing on the same protocol.
Conclusion The weekly etoposide and platinum chemotherapy is a practical and feasible treatment option in patients who are otherwise fragile and unfit for standard-dose chemotherapy.
Pathways of initial consonant loss
Authors: Verstraete Jean-Christophe 
Published: September 2021

AbstractThis paper investigates the historical loss of root-initial consonants, using a case study of Middle Paman languages of Cape York Peninsula, in northeastern Australia. Systematic loss of initial consonants is a typologically unusual phenomenon, mainly found in Australia, that has often been regarded as a starting point for far-reaching changes in root structure, phonotactics and even phoneme inventory. So far, the literature has focused mainly on identifying phonetic causes of initial loss. This study focuses on the actual processes and pathways of initial loss, which is an equally important part of the historical puzzle. Specifically, it shows that there are multiple pathways for initial loss: it can be the result of a gradual phonetic process involving intermediate steps like lenition, as is assumed in part of the literature, but it can also be due to more abrupt processes involving borrowing and even morphosyntactic alternations. This adds to a more diversified model of how initial loss actually proceeds, which together with earlier work on the diversity of phonetic causes of initial loss produces a more comprehensive understanding of this typologically and diachronically unusual phenomenon.
Strong interplay between superluminosity and radiation friction during direct laser acceleration
Authors: Yeh I-L , Tangtartharakul K , Rinderknecht H G , Willingale L , Arefiev A 
Published: September 2021

Abstract
Using a test-particle model, we examine direct laser acceleration of electrons within a magnetic filament that has been shown to form inside a laser-irradiated plasma. We focus on ultra-high intensity interactions where the force of radiation friction caused by electron emission of electromagnetic radiation must be taken into account. It is shown that even relatively weak superluminosity of laser wave fronts—the feature that has been previously neglected—qualitatively changes the electron dynamics, leading to a so-called attractor effect. As a result of this effect, electrons with various initial energies reach roughly the same maximum energy and emit roughly the same power in the form of x-rays and gamma-rays. Our analysis implies that the primary cause of the superluminosity is the laser-heated plasma. The discovered strong interplay between superluminosity and radiation friction is of direct relevance to laser-plasma interactions at high-intensity multi-PW laser facilities.
Numerical investigation of a new approach based on perovskite CH3NH3PbI3 absorber layer for high-efficiency solar cells
Authors: Sadiq Muhammad , Naeem Khan Muhammad , Arif Muhammad , Naveed Amir , Ullah Kaleem , Afridi Shaista 
Published: September 2021

Abstract
Recently, metal halide perovskite materials for solar cells have gained a wonderful attention from researchers around the world. In this paper, a novel perovskite layer in combination with other layers is numerically investigated to enhance the performance of perovskite-based solar cells (PSCs). General-purpose photovoltaic device model (GPVDM) is used to simulate the proposed structure with Methylammonium Lead Iodide (CH3NH3PbI3), sandwiched between a bi- and tri-layer. The results show enhanced short circuit current density (J

sc
) and power conversion efficiency (PCE) for PSCs. The proposed PSCs show a Jsc of 39.6 mA cm−2 and PCE 31.4% under standard AM 1.5 G. The bi- and tri-layer sandwiched CH3NH3PbI3 structure is an elegant solution for the realization of high efficiency PSCs.
Volume ratios for Cartesian products of convex bodies
Authors: Khrabrov A. 
Published: September 2021

The paper is devoted to the behavior of volume ratios, the modified Banach–Mazur distance, and the vertex index for sums of convex bodies. It is shown that

sup
d
(

A

⊕

K

,

B

⊕

L

)
≥
sup
∂
(

A

⊕

K

,

B

⊕

L

)
≥
c
⋅

n

1
−

k
+

k
′

2
n

,

\begin{equation*} \sup d (\mathrm {A}\oplus \mathrm {K},\mathrm {B}\oplus \mathrm {L}) \geq \sup \partial (\mathrm {A}\oplus \mathrm {K},\mathrm {B}\oplus \mathrm {L}) \geq c \cdot n^{1-\frac {k+k’}{2n}}, \end{equation*}

if

K

⊂

R

n

\mathrm {K}\subset \mathbb {R}^n

and

L

⊂

R

k

\mathrm {L}\subset \mathbb {R}^k

are convex and symmetric (the supremum is taken over all symmetric convex bodies

A

⊂

R

n
−
k

\mathrm {A}\subset \mathbb {R}^{n-k}

and

B

⊂

R

n
−

k
′

)

\mathrm {B}\subset \mathbb {R}^{n-k’})

. Furthermore, some examples are discussed that show that the available extimates of the vertex index in terms of the volume ratio are not sharp.
Inner factors of analytic functions of variable smoothness in the closed disk
Authors: Shirokov N. 
Published: September 2021

Let

p
(
ζ
)

p(\zeta )

be a positive function defined on the unit circle

T

\mathbb {T}

and satisfying the condition

|

p
(

ζ
2

)
−
p
(

ζ
1

)

|

≤

c
0

log
⁡

e

|

ζ
2

−

ζ
1

|

,

ζ
1

,

ζ
2

∈

T

,

\begin{equation*} |p(\zeta _2)-p(\zeta _1)|\le \frac {c_0}{\log \frac {e} {|\zeta _2-\zeta _1|}}, \quad \zeta _1,\zeta _2\in \mathbb {T}, \end{equation*}

p
−

=

min

ζ
∈

T

p
(
ζ
)

p_-=\min _{\zeta \in \mathbb {T}}p(\zeta )

. Futhermore, let

0
>
α
>
1

0>\alpha >1

,

r
≥
0

r\ge 0

,

r
∈

Z

r\in \mathbb {Z}

, and assume that

p
−

>

1
α

p_->\frac {1}{\alpha }

. Define a class of analytic functions in the unit disk

D

\mathbb {D}

as follows:

f
∈

H

r
+
α

p
(

⋅

)

f\in H^{p(\,\cdot \,)}_{r+\alpha }

if

sup

0
>
ρ
>
1

sup

0
>

|

θ

|

>
π

∫
0

2
π

|

f

(
r
)

(
ρ

e

i
(
λ
+
θ
)

)
−

f

(
r
)

(
ρ

e

i
λ

)

|

θ

|

α

|

p
(

e

i
λ
)

d
λ
>
∞
.

\begin{equation*} \sup _{0>\rho >1}\,\sup _{0>|\theta |>\pi } \int ^{2\pi }_0 \bigg |\frac {f^{(r)}(\rho e^{i(\lambda +\theta )})-f^{(r)}(\rho e^{i\lambda })} {|\theta |^{\alpha }}\bigg |^{p(e^{i\lambda )}}\,d\lambda >\infty . \end{equation*}

The following main results are proved.

Theorem 1. Let

f
∈

H

r
+
α

p
(

⋅

)

,

f\in H^{p(\,\cdot \,)}_{r+\alpha },

and let

I
I

be an inner function,

f

/

I
∈

H
1

f/I\in H^1

. Then

f

/

I
∈

H

r
+
α

p
(

⋅

)

f/I\in H^{p(\,\cdot \,)}_{r+\alpha }

.

Theorem 2. Let

f
∈

H

r
+
α

p
(

⋅

)

,

f\in H^{p(\,\cdot \,)}_{r+\alpha },

and let

I
I

be an inner function,

f

/

I
∈

H

∞

f/I\in H^{\infty }

. Assume that the multiplicity of every zero of

f
f

in

D

\mathbb {D}

is at least

r
+
1

r+1

. Then

f
I
∈

H

r
+
α

p
(

⋅

)

fI\in H^{p(\,\cdot \,)}_{r+\alpha }

.
FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases
Authors: Delmas Maxime , Filangi Olivier , Paulhe Nils , Vinson Florence , Duperier Christophe , Garrier William , Saunier Paul-Emeric , Pitarch Yoann , Jourdan Fabien , Giacomoni Franck , Frainay Clément 
Published: September 2021

Abstract

Motivation
Metabolomics studies aim at reporting a metabolic signature (list of metabolites) related to a particular experimental condition. These signatures are instrumental in the identification of biomarkers or classification of individuals, however their biological and physiological interpretation remains a challenge. To support this task, we introduce FORUM: a Knowledge Graph (KG) providing a semantic representation of relations between chemicals and biomedical concepts, built from a federation of life science databases and scientific literature repositories.

Results
The use of a Semantic Web framework on biological data allows us to apply ontological-based reasoning to infer new relations between entities. We show that these new relations provide different levels of abstraction and could open the path to new hypotheses. We estimate the statistical relevance of each extracted relation, explicit or inferred, using an enrichment analysis, and instantiate them as new knowledge in the KG to support results interpretation/further inquiries.

Availability and implementation
A web interface to browse and download the extracted relations, as well as a SPARQL endpoint to directly probe the whole FORUM KG, are available at https://forum-webapp.semantic-metabolomics.fr. The code needed to reproduce the triplestore is available at https://github.com/eMetaboHUB/Forum-DiseasesChem.

Supplementary information
Supplementary data are available at Bioinformatics online.
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding
Authors: Xu Gang , Wang Qinghua , Ma Jianpeng 
Published: September 2021

Abstract

Motivation
The development of an open-source platform to predict protein 1D features and 3D structure is an important task. In this paper, we report an open-source toolkit for protein 3D structure modeling, named OPUS-X. It contains three modules: OPUS-TASS2, which predicts protein torsion angles, secondary structure and solvent accessibility; OPUS-Contact, which measures the distance and orientation information between different residue pairs; and OPUS-Fold2, which uses the constraints derived from the first two modules to guide folding.

Results
OPUS-TASS2 is an upgraded version of our previous method OPUS-TASS. OPUS-TASS2 integrates protein global structure information and significantly outperforms OPUS-TASS. OPUS-Contact combines multiple raw co-evolutionary features with protein 1D features predicted by OPUS-TASS2, and delivers better results than the open-source state-of-the-art method trRosetta. OPUS-Fold2 is a complementary version of our previous method OPUS-Fold. OPUS-Fold2 is a gradient-based protein folding framework based on the differentiable energy terms in opposed to OPUS-Fold that is a sampling-based method used to deal with the non-differentiable terms. OPUS-Fold2 exhibits comparable performance to the Rosetta folding protocol in trRosetta when using identical inputs. OPUS-Fold2 is written in Python and TensorFlow2.4, which is user-friendly to any source-code-level modification.

Availabilityand implementation
The code and pre-trained models of OPUS-X can be downloaded from https://github.com/OPUS-MaLab/opus_x.

Supplementary information
Supplementary data are available at Bioinformatics online.
utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation
Authors: Liu Yating , Dougherty Joseph D 
Published: September 2021

Abstract

Summary
Whole genome sequencing of patient populations is identifying thousands of new variants in untranslated regions (UTRs). While the consequences of UTR mutations are not as easily predicted from primary sequence as coding mutations are, there are some known features of UTRs that modulate their function. utr.annotation is an R package that can be used to annotate potential deleterious variants in the UTR regions for both human and mouse species. Given a CSV or VCF format variant file, utr.annotation provides information of each variant on whether and how it alters known translational regulators including upstream open reading frames, upstream Kozak sequences, polyA signals, Kozak sequences at the annotated translation start site, start codons and stop codons, conservation scores in the variant position, and whether and how it changes ribosome loading based on a model derived from empirical data.

Availability and implementation
utr.annotation is freely available on Bitbucket (https://bitbucket.org/jdlabteam/utr.annotation/src/master/) and CRAN (https://cran.r-project.org/web/packages/utr.annotation/index.html).

Supplementary information
Supplementary data are available at Bioinformatics online.