bluuebunny/crossref_metadata_2025 huggingface dataset:
Global topographic uplift has elevated speciation in mammals and birds over the last 3 million years
Authors: Igea Javier , Tanentzap Andrew J.
Published: September 2021

Topographic change shapes the evolution of biodiversity by influencing both habitat connectivity and habitat diversity as well as abiotic factors like climate. However, its role in creating global biodiversity gradients remains poorly characterized because geology, climate and evolutionary data have rarely been integrated across concordant timescales. Here we show that topographic uplift over the last 3 million years explains more spatial variation in the speciation of all mammals and birds than do the direct effects of palaeoclimate change and both present-day elevation and present-day temperature. By contrast, the effects of topographic changes are much smaller than those of present-day temperatures in eroded areas. Together, our results stress that historical geological processes rather than traditionally studied macroecological gradients may ultimately generate much of the world’s biodiversity. More broadly, as the Earth’s surface continues to rise and fall, topography will remain an important driver of evolutionary change and novelty.
The emergence of heterogeneous scaling in research institutions
Authors: Burghardt Keith A. , He Zihao , Percus Allon G. , Lerman Kristina
Published: September 2021

Research institutions provide the infrastructure for scientific discovery, yet their role in the production of knowledge is not well characterized. To address this gap, we analyze interactions of researchers within and between institutions from millions of scientific papers. Our analysis reveals that collaborations densify as each institution grows, but at different rates (heterogeneous densification). We also find that the number of institutions scales with the number of researchers as a power law (Heaps’ law) and institution sizes approximate Zipf’s law. These patterns can be reproduced by a simple model in which researchers are preferentially hired by large institutions, while new institutions complimentarily generate more new institutions. Finally, new researchers form triadic closures with collaborators. This model reveals an economy of scale in research: larger institutions grow faster and amplify collaborations. Our work deepens the understanding of emergent behavior in research institutions and their role in facilitating collaborations.
Electron-withdrawing group modified carbazolophane donors for deep blue thermally activated delayed fluorescence OLEDs
Authors: Gupta Abhishek Kumar , Zhang Zhen , Spuling Eduard , Kaczmarek Maria , Wang Yichuan , Hassan Zahid , Samuel Ifor D. W. , Bräse Stefan , Zysman-Colman Eli
Published: September 2021

We report two blue-emitting thermally activated delayed fluorescence (TADF) compounds employing a substituted carbazolophane (Czp) donor (indolo[2.2]paracyclophane).
“PP-type” self-assembling peptides with superior rheological properties
Authors: Li Fangmin , Gao Lichang , Zhang Xudong , Wang Pin , Liu Yuanxue , Feng Jinhui , Zhang Chunxia , Zhao Chengru , Zhang Shang
Published: September 2021

Proline terminated "PP-type" self-assembling peptides have better flowability before gel forming and equivalent gel strength after gel forming.
High-efficiency electro-catalytic performance of green dill biochar cathode and its application in electro-Fenton process for the degradation of pollutants
Authors: Tao Ling , Ren Hanru , Yu Fangke
Published: September 2021

Biochar (BC) is a kind of carbon-rich, renewable and low-cost material, which can be prepared from various organic materials.
Vinylnaphthalene-bearing hexaoxazole as a fluorescence turn-on type G-quadruplex ligand
Authors: Ma Yue , Wakabayashi Yuki , Watatani Naruyuki , Saito Ryota , Hirokawa Takatsugu , Tera Masayuki , Nagasawa Kazuo
Published: September 2021

Cyclic hexaoxazoles bearing vinyl naphthalene moiety is developed as a fluoresence turn-on ligand selectively against G-quadruplex.
Tuning the electrochemical and catalytic ORR performance of C60by its encapsulation in ZIF-8: a solid-state analogue of dilute fullerene solution
Authors: Basu Olivia , Mukhopadhyay Subhabrata , De Avik , Das Anupam , Das Samar K.
Published: September 2021

Hassle-free encapsulation of fullerene C60in ZIF-8 has been performed to preserve the molecularity and solution-like properties of C60in solid-state. The resulting composite shows efficient heterogeneous electrocatalytic oxygen reduction reaction.
Confining lead-free perovskite quantum dots in metal–organic frameworks for visible light-driven proton reduction
Authors: Wang Yao-Yao , Ji Xue-Yang , Yu Meng , Tao Jun
Published: September 2021

Lead-free perovskite quantum dots are introduced into metal–organic framework photocatalysts through an anti-solvent recrystallization method for high photocatalytic performance under visible light.
In situ formation of a molecular cobalt(iii)/AgCl photocatalyst for visible-light water oxidation
Authors: Mogi Hiroto , Okazaki Megumi , Nishioka Shunta , Maeda Kazuhiko
Published: September 2021

A unique photocatalyst that consists of a molecular Co(iii) species and wide-bandgap AgCl is presented. Even without a physical connection between the two components, the Co(iii)/AgCl photocatalyst showed water oxidation activity under visible light.
MXene aerogel for efficient photothermally driven membrane distillation with dual-mode antimicrobial capability
Authors: Cao Sisi , Wu Xuanhao , Zhu Yaguang , Gupta Prashant , Martinez Adrian , Zhang Yunzhu , Ghim Deoukchen , Wang Yixuan , Liu Lin , Jun Young-Shin , Singamaneni Srikanth
Published: September 2021

A MXene-based composite aerogel enabling highly efficient photothermally driven membrane distillation with dual-mode anti-biofouling properties make it highly appealing for solar-driven desalination.
Dysphagia, COVID-19, and the Clinical Swallow Evaluation: Consistently Inconsistent
Authors: Schwartz Talia H.
Published: September 2021

Purpose

Dysphagia management in COVID-19 patients during the New York City spring surge in early 2020 was challenging for many speech-language pathologists, as instrumental swallow evaluations were unavailable. Renewed attention was brought to the value of the clinical swallow evaluation.

Conclusion

While consistently utilized, the experience also brought back into light the inconsistences in which the clinical swallow evaluation is executed.
Overall bone gaining after using calcium sulfate bone graft simultaneously to dental implantation
Authors: Saoud Kenan , Brad Bassel , Alkhouli Muaaz
Published: September 2021

Objectives: this study was carried out to evaluate the gaining occurring in the bone gaining after the simultaneous grafting with calcium sulfate around dental implants. Materials and methods: 24 implantation sites in the anterior area of the maxilla were included in this study. Dental implants were inserted, bone grafting was done simultaneously and post evaluation of the overall bone gaining 6 months after the grafting process (T2 time) was done to study the changes. Results: Paired Samples T-Test revealed a significant difference between the three time points (before the implantation, the day after it, six months later) (P-value = 0.000) at the confidence level of 95%. Furthermore, two-way comparisons between the three follow-ups was done to determine where the difference was. The test showed that there is a significant difference (P-value < 0.05) between all time points. by doing two-way comparisons between the three follow-ups, it was shown that the significant difference (P-value < 0.05) was in each comparison. Conclusion: We conclude within the limits of this study that an adequate amount of bone gain was found 6 months after the bone grafting process.
Significance of cervical node necrosis in preoperative MRI as a prognostic indicator: retrospective study of patients with SCC of tongue
Authors: Dhara Vasantha , Hoda Nadimul , Rajini BC , Sabitha KS , Vinitha A , Nathani Jayesh
Published: September 2021

Aim:To ascertain the prognostic value of cervical nodal necrosis (CNN) observed in patients of tongue squamous cell carcinoma with magnetic resonance imaging.Materials and methods:In this retrospective observational study, records of 144 patients diagnosed with newly diagnosed SCC of tongue were considered. Preoperative MRI study, demographic and clinical data were reviewed. Based on MRI reports, patients were categorised into: with or without the presence of cervical node necrosis (CNN or non CNN). Subsequent treatments, histopathological reports and follow up data were studied to determine key prognostic elements, overall survival and disease free survival by statistical analysis.Results:The incidence of CNN was 55.55% in the study sample. CNN category, depth of invasion, N stage and extra nodal extension were significant negative prognostic factors for overall and disease free survival.Conclusion:Based on our results, pre operative MRI based presence of cervical node necrosis in tongue squamous cell carcinoma is an independent prognostic indicator for poor overall and disease free survival. Long term prospective studies with larger cohorts could be undertaken to establish its role as an important biomarker for precision treatments.
Contrast-Enhanced Ultrasound Improves the Accuracy of the ACR TI-RADS in the Diagnosis of Thyroid Nodules Located in the Isthmus
Authors: Huang Yunlin , Hong Yurong , Xu Wen , Song Kai , Huang Pintong
Published: September 2021

Objectives To evaluate the diagnostic performance of the American College of Radiology (ACR) Thyroid Image Reporting and Data System (TI-RADS), contrast-enhanced ultrasound (CEUS), and a modified TI-RADS in differentiating benign and malignant nodules located in the isthmus.

Methods This retrospective study was approved by the institutional review board. Informed consent was obtained. Grayscale ultrasound (US) and CEUS images were obtained for 203 isthmic thyroid nodules (46 benign and 157 malignant) in 198 consecutive patients (156 women, mean age: 44.7 years ± 11.3 [standard deviation]; 47 men, mean age: 40.9 years ± 11.0). The area under the receiver operating characteristic curve (AUC) of the diagnostic performance of the ACR TI-RADS, CEUS, and the modified TI-RADS were evaluated.

Results Lobulated or irregular margins (P = 0.001; odds ratio [OR] = 9.250) and punctate echogenic foci (P = 0.007; OR = 4.718) on US and hypoenhancement (P < 0.001; OR = 20.888) on CEUS displayed a significant association with malignancy located in the isthmus. The most valuable method to distinguish benign nodules from malignant nodules was the modified TI-RADS (AUC: 0.863 with modified TR5), which was significantly better than the ACR TI-RADS (AUC: 0.738 with ACR TR5) (P < 0.001) but showed no significant difference with respect to CEUS (AUC: 0.835 with hypoenhancement) (P = 0.205). The diagnostic value was significantly different between CEUS and the ACR TI-RADS (P = 0.028).

Conclusion The modified TI-RADS could significantly improve the accuracy of the diagnosis of thyroid nodules located in the isthmus.
The Use and Promise of Conversational Agents in Digital Health
Authors: Dingler Tilman , Kwasnicka Dominika , Wei Jing , Gong Enying , Oldenburg Brian
Published: September 2021

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

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

Robotic 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

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

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.
Fiber optics offer better photoacoustic detection
Authors: Patrick Chris
Published: September 2021

An optical coherence photoacoustic microscopy system uses a fiber-based dome sensor to noninvasively image zebrafish larvae.
Vital nodes identification can simplify plasma chemistry to streamline biomedicine studies
Authors: Ikenson Ben
Published: September 2021

Promising AI method for simplifying identification of key plasma chemicals may pioneer advancements in biomedicine.
Reconsidering power functional theory
Authors: Lutsko James F. , Oettel Martin
Published: September 2021

The original derivation of power functional theory [M. Schmidt and J. M. Brader, J. Chem. Phys. 138, 214101 (2013)] is reworked in some detail with a view to clarifying and simplifying the logic and making explicit the various functional dependencies. We note various issues with the original development and suggest a modification that allows us to avoid them. In the process, we also suggest an alternative interpretation of our results, which bears surprising similarities to classical density functional theory.
Classical threshold law for the formation of van der Waals molecules
Authors: Mirahmadi Marjan , Pérez-Ríos Jesús
Published: September 2021

We study the role of pairwise long-range interactions in the formation of van der Waals molecules through direct three-body recombination processes A + B + B → AB + B, based on a classical trajectory method in hyperspherical coordinates developed in our earlier works [J. Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014); M. Mirahmadi and J. Pérez-Ríos, J. Chem. Phys. 154, 034305 (2021)]. In particular, we find the effective long-range potential in hyperspherical coordinates with an exact expression in terms of dispersion coefficients of pairwise potentials. Exploiting this relation, we derive a classical threshold law for the total cross section and the three-body recombination rate yielding an analytical expression for the three-body recombination rate as a function of the pairwise long-range coefficients of the involved partners.
Pathways of initial consonant loss
Authors: Verstraete Jean-Christophe
Published: September 2021

This 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

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.
Corrigendum: Extreme ultraviolet spectroscopy of highly charged argon ions at the Berlin EBIT (Biedermann, Radtke, Fussmann, Allen 2007 J. Phys. Conf. Ser. 72 012004)
Authors: Biedermann C.
Published: September 2021

Please see Article PDF for corrigendum text.
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

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.
Singular matrix conjugacy problem with rapidly oscillating off-diagonal entries. Asymptotics of the solution in the case when a diagonal entry vanishes at a stationary point
Authors: Budylin A.
Published: September 2021

The

(
2
×
2
)

(2\times 2)

matrix conjugacy problem (the Riemann–Hilbert problem) with rapidly oscillating off-diagonal entries and quadratic phase function is considered, specifically, the case when one of the diagonal entries vanishes at a stationary point. For solutions of this problem, the leading term of the asymptotics is found. However, the method allows us to construct complete expansions in power orders. These asymptotics can be used, for example, to construct the asymptotics of solutions of the Cauchy problem for the nonlinear Schrödinger equation for large times in the case of the so-called collisionless shock region.
On (2,3)-generation of matrix groups over the ring of integers, II
Authors: Vsemirnov M.
Published: September 2021

Final steps are done in proving that the groups

SL
⁡
(
n
,

Z

)

\operatorname {SL}(n,\mathbb {Z})

,

GL
⁡
(
n
,

Z

)

\operatorname {GL}(n,\mathbb {Z})

and

PGL
⁡
(
n
,

Z

)

\operatorname {PGL}(n,\mathbb {Z})

are

(
2
,
3
)

(2,3)

-generated if and only if

n
≥
5

n\ge 5

, and

PSL
⁡
(
n
,

Z

)

\operatorname {PSL}(n,\mathbb {Z})

is

(
2
,
3
)

(2,3)

-generated if and only if

n
=
2

n=2

or

n
≥
5

n\ge 5

. In particular, the results cover the remaining cases of

n
=
8

n=8

, …,

12
12

, and

14
14

.
A cellular structure of the space of branched coverings for the two-dimensional sphere
Authors: Zvonilov V. , Orevkov S.
Published: September 2021

For a closed oriented surface

Σ
\Sigma

, let

X

Σ
,
n

X_{\Sigma , n}

be the space of isomorphism classes of

n
n

-fold orientation preserving branched coverings

Σ
→

S
2

\Sigma \rightarrow S ^2

of the two-dimensional sphere. Earlier, the authors constructed a compactification

X
¯

Σ
,
n

\overline {X}_{\Sigma , n}

of this space, which coincides with the Diaz–Edidin–Natanzon–Turaev compactification of the Hurwitz space

H
(
Σ
,
n
)
⊂

X

Σ
,
n

H (\Sigma , n) \subset X_{\Sigma , n}

that consists of isomorphism classes of branched coverings with all critical values being simple. With the help of Grothendieck’s dessins d’enfants, a cellular structure of this compactification is constructed. The results obtained are applied to the space of trigonal curves on an arbitrary Hirzebruch surface.
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
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sup d left-parenthesis normal upper A circled-plus normal upper K comma normal upper B circled-plus normal upper L right-parenthesis greater-than-or-equal-to sup partial-differential left-parenthesis normal upper A circled-plus normal upper K comma normal upper B circled-plus normal upper L right-parenthesis greater-than-or-equal-to c dot n Superscript 1 minus StartFraction k plus k Super Superscript prime Superscript Over 2 n EndFraction Baseline comma">

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
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartAbsoluteValue p left-parenthesis zeta 2 right-parenthesis minus p left-parenthesis zeta 1 right-parenthesis EndAbsoluteValue less-than-or-equal-to StartStartFraction c 0 OverOver log StartFraction e Over StartAbsoluteValue zeta 2 minus zeta 1 EndAbsoluteValue EndFraction EndEndFraction comma zeta 1 comma zeta 2 element-of double-struck upper T comma">

|

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
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="sup Underscript 0 greater-than rho greater-than 1 Endscripts sup Underscript 0 greater-than StartAbsoluteValue theta EndAbsoluteValue greater-than pi Endscripts integral Subscript 0 Superscript 2 pi Baseline StartAbsoluteValue StartFraction f Superscript left-parenthesis r right-parenthesis Baseline left-parenthesis rho e Superscript i left-parenthesis lamda plus theta right-parenthesis Baseline right-parenthesis minus f Superscript left-parenthesis r right-parenthesis Baseline left-parenthesis rho e Superscript i lamda Baseline right-parenthesis Over StartAbsoluteValue theta EndAbsoluteValue Superscript alpha Baseline EndFraction EndAbsoluteValue Superscript p left-parenthesis e Super Superscript i lamda right-parenthesis Superscript Baseline d lamda greater-than normal infinity period">

sup

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sup

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|

θ

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π

∫
0

2
π

|

f

(
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)

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(
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−

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\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

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

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

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.
High-throughput sequencing reveals dietary segregation in Malaysian babblers
Authors: Mansor Mohammad Saiful , Rozali Fasihah Zarifah , Davies Sian , Nor Shukor Md , Ramli Rosli
Published: September 2021

The coexistence of numerous species within a community results from how those species use available resources. Babblers are one of the major groups of Malaysian insectivorous birds, which frequently forage in dense vegetation cover and have a high level of sympatry. Therefore, examining the diet, prey selection, and niche segregation of babblers can be challenging. In this study, we used high-throughput sequencing to investigate potential dietary overlap or segregation among 10 babbler species of the 4 genera of the family Pellorneidae and Timaliidae: Pellorneum, Malacopteron, Stachyris, and Cyanoderma in central peninsular Malaysia. We tested the hypothesis that trophically similar species may differ in resource use to avoid competitive exclusion. We identified 81 distinct arthropod taxa from fecal samples, belonging to 71 families representing 13 orders, which were predominantly from 16 dipteran, 13 lepidopteran, and 10 coleopteran families. Of all the prey taxa consumed, 45% were found to be distinct across the 10 babbler species, and ˂35% were shared simultaneously by ≥3 babbler species, indicating minimal dietary overlap. The black-throated babbler Stachyris nigricollis and moustached babbler Malacopteron magnirostre had the most generalist tendencies because they consumed a greater variety of prey taxa. Small dietary overlap values (Ojk) and a relatively wide range of food resources suggest that dietary segregation occurred among the studied babblers. The great diversity of prey consumed revealed the presence of dietary flexibility among the sympatric insectivorous birds, thus reducing any active dietary competition and facilitating the coexistence through niche partitioning.
Randomized controlled trial of once-per-week intermittent fasting for health improvement: the WONDERFUL trial
Authors: Bartholomew Ciera L , Muhlestein Joseph B , May Heidi T , Le Viet T , Galenko Oxana , Garrett Kelly Davis , Brunker Cherie , Hopkins Ramona O , Carlquist John F , Knowlton Kirk U , Anderson Jeffrey L , Bailey Bruce W , Horne Benjamin D
Published: September 2021

Aims

Low-density lipoprotein cholesterol (LDL-C) predicts heart disease onset and may be reduced by intermittent fasting. Some studies, though, reported that fasting increased LDL-C; however, no study evaluated LDL-C as the primary endpoint. This randomized controlled trial evaluated the effect of low-frequency intermittent fasting on LDL-C and other biomarkers.

Methods and results

Adults aged 21–70 years were enrolled who were not taking a statin, had modestly elevated LDL-C, had ≥1 metabolic syndrome feature or type 2 diabetes, and were not taking anti-diabetic medication (N = 103). Water-only 24-h fasting was performed twice weekly for 4 weeks and then once weekly for 22 weeks; controls ate ad libitum. The primary outcome was 26-week LDL-C change score. Secondary outcomes (requiring P ≤ 0.01) were 26-week changes in homeostatic model assessment of insulin resistance (HOMA-IR), Metabolic Syndrome Score (MSS), brain-derived neurotrophic factor (BDNF), and MicroCog general cognitive proficiency index (GCPi). Intermittent fasting (n = 50) and control (n = 53) subjects were, respectively, aged 49.3 ± 12.0 and 47.0 ± 9.8 years, predominantly female (66.0% and 67.9%), and overweight (103 ± 24 and 100 ± 21 kg) and had modest LDL-C elevation (124 ± 19 and 128 ± 20 mg/dL). Drop-outs (n = 12 fasting, n = 20 control) provided an evaluable sample of n = 71 (n = 38 fasting, n = 33 control). Intermittent fasting did not change LDL-C (0.2 ± 16.7 mg/dL) vs. control (2.5 ± 19.4 mg/dL; P = 0.59), but it improved HOMA-IR (−0.75 ± 0.79 vs. −0.10 ± 1.06; P = 0.004) and MSS (−0.34 ± 4.72 vs. 0.31 ± 1.98, P = 0.006). BDNF (P = 0.58), GCPi (P = 0.17), and weight (−1.7 ± 4.7 kg vs. 0.2 ± 3.5 kg, P = 0.06) were unchanged.

Conclusions

A low-frequency intermittent fasting regimen did not reduce LDL-C or improve cognitive function but significantly reduced both HOMA-IR and MSS.

Trial registration

 clinicaltrials.gov, NCT02770313.
Multivariate Model Update Chemometric Methods for Determination of Prednisolone and Esomeprazole in Spiked Human Plasma: A Comparative Study
Authors: Farid Nehal F , Magdy Maimana A , Anwar Basma H , Abdelhamid Nessreen S
Published: September 2021

Background

Prednisolone (PRD) is an immunosuppressant and anti-inflammatory drug, although it may cause peptic ulcers as a side effect. Esomeprazole (ESO) is used for the treatment of peptic ulcers, therefore the two drugs are co-administered in cases of organ transplantation and autoimmune diseases.

Objective

This work aims to determine the two drugs simultaneously, in bulk, and in spiked human plasma by eliminating the overlap of their spectra and the interference of the plasma matrix.

Methods

Two simple and effective updated chemometric models—principal component analysis (PCA) and partial least squares (PLS)—were established using UV spectrophotometric data.

Results

The two updated models have been validated according to the U.S. Food and Drug Administration guidelines with acceptable results. The results were statistically compared with those of the reported methods, where no significant difference was found, indicating the validity of the developed methods. The two updated models have been successfully applied for prediction of the proposed drugs with good accuracy and precision.

Conclusion

The two updated models are simple, rapid, sensitive, and precise and could be easily applied in quality control laboratories for determination of PRD and ESO, without any preliminary separation steps or interference from plasma matrixes.

Highlights

Two model updated chemometric models, PCA and PLS, were established for determination of PRD and ESO in spiked human plasma using UV spectrophotometric data.
Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene
Authors: Vesco Guglielmo , Lamperti Marco , Salerno Domenico , Marrano Claudia Adriana , Cassina Valeria , Rigo Riccardo , Buglione Enrico , Bondani Maria , Nicoletto Giulia , Mantegazza Francesco , Sissi Claudia , Nardo Luca
Published: September 2021

G-quadruplexes embedded within promoters play a crucial role in regulating the gene expression. KIT is a widely studied oncogene, whose promoter contains three G-quadruplex forming sequences, c-kit1, c-kit2 and c-kit*. For these sequences available studies cover ensemble and single-molecule analyses, although for kit* the latter were limited to a study on a promoter domain comprising all of them. Recently, c-kit2 has been reported to fold according to a multi-step process involving folding intermediates. Here, by exploiting fluorescence resonance energy transfer, both in ensemble and at the single molecule level, we investigated the folding of expressly designed constructs in which, alike in the physiological context, either c-kit2 or c-kit* are flanked by double stranded DNA segments. To assess whether the presence of flanking ends at the borders of the G-quadruplex affects the folding, we studied under the same protocols oligonucleotides corresponding to the minimal G-quadruplex forming sequences. Data suggest that addition of flanking ends results in biasing both the final equilibrium state and the folding kinetics. A previously unconsidered aspect is thereby unravelled, which ought to be taken into account to achieve a deeper insight of the complex relationships underlying the fine tuning of the gene-regulatory properties of these fascinating DNA structures.