bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solving inverse problems in physics by optimizing a discrete loss is much more faster and accurate without neural networks
Authors: Karnakov Petr , Litvinov Sergey , Koumoutsakos Petros 
Published: November 2022

Abstract
In recent years there is a wealth of activities for solving inverse problems in physics described by partial differential equations (PDEs) using neural networks (NNs). In these efforts, the solution of the PDEs are expressed as NNs that are trained through the minimization of a loss function involving the PDE. Here we show how to accelerate this approach by five orders of magnitude by deploying, instead of NNs, classical PDE approximations that are facilitated by machine learning tools. The framework of Optimizing a Discrete Loss (ODIL), minimizes a cost function for discrete approximations of the PDEs using gradient-based and Gauss-Newton methods. The framework relies on grid-based discretizations of PDEs and inherits their accuracy, convergence, and conservation properties. The implementation of the method is facilitated by adopting broadly accessible machine learning tools for automatic differentiation. We present applications to PDE-constrained optimization, optical flow, system identification, and data assimilation. We compare ODIL with the popular method of Physics Informed Neural Networks (PINNS) and show that it outperforms it by up to five orders of magnitude in computational speed while having better accuracy and convergence rates. We evaluate the method on various forward and inverse problems involving linear and nonlinear partial differential equations including the Navier-Stokes equations for flow reconstruction problems. The present framework interfaces numerical methods and machine learning and presents a powerful tool for solving effectively challenging inverse problems across scientific domains.
A Note on the Correct View of Adiabatic Process
Authors: Bharathraj Goddalehundi 
Published: November 2022

Abstract
Note: Please see pdf for full abstract with equations
An adiabatic process is described as a thermodynamic process where there is no exchange of heat or mass between the system and its surroundings. However there will be an exchange of mechanical work. In this article we specifically consider a class of adiabatic processes where the imposed external pressure remains constant until the system pressure comes in equilibrium with the imposed external pressure. We normally use the expression PVγ = Constant to describe such processes, but surprisingly it does not satisfy the 1st Law of Thermodynamics. If Pi, Pƒ are the initial and final state Pressure and Vi, Vƒ are the initial and final state Volume of gas in a cylinder, then the correct expression we get is Vƒ = Vi(1 + Pi/Pƒ ƒ/2) / (1 + ƒ/2), where ƒ = degree of freedom of the gas molecules. Also note, γ = (ƒ +2) / ƒ. We can also derive PiVγi = PƒVγƒ when Pƒ ≈ Pi in the correct expression. Another point we can note is this process is inherently irreversible.
HeliDye1: helquat fluorogenic probe specific for AT-rich DNA duplexes
Authors: Kužmová Erika , Joshi Vishwas , Kozák Jaroslav , Severa Lukáš , Bednarova Lucie , Yurenko Yevgen , Dobiaš Juraj , Pecina Adam , Köprülüoğlu Cemal , Jurečka Petr , Lepšík Martin , Hobza Pavel , Cisarova Ivana , Pohl Radek , Jurkiewicz Piotr , Cebecauer Marek , Trojanec Radek , Dzubak Petr , Hajduch Marian , Teplý Filip , Reyes-Gutiérrez Paul , Zawada Zbigniew 
Published: November 2022

Abstract
DNA-binding fluorescent probes are useful tools in cell biology for various applications enabling visualisation and quantification of DNA. Herein, we report on HeliDye1, a novel cationic helicene-like DNA probe, and its versatile usability. HeliDye1 exhibits fluorescence exclusively in the presence of DNA duplexes containing AT base pairs and (contrary to any recent DNA probe) it remains non-fluorescent in the presence of single-stranded DNA and RNA. Favourable chemical properties of HeliDye1 allowed its use in super-resolution microscopy and DNA quantification using flow cytometry. We present five more applications of HeliDye1. Viscosimetry showed that HeliDye1 is a minor groove binder. HeliDye1 interacts with double-stranded DNA as an induced (P)-enantiomer, which we confirmed by ECD spectroscopy and DFT calculations. ECD spectroscopy suggested the formation of HeliDye1 dimers. MD simulations predicted the structures of (P)-HeliDye1 dimers inside DNA and showed their stability in AT-rich sequences and instability in GC-rich sequences.
What determines the success of rural water supply schemes? Insights from an assessment in Maharashtra
Authors: Kabir Yusuf , Ghodke Anand , Kumar Saurabh 
Published: November 2022

Abstract
The article discusses a statistical model to explain the varying performance of water supply schemes under different physical environments in the state of Maharashtra in India, characterized by high spatial and temporal variability in rainfall and climate, and heterogeneity in geological and geomorphological conditions. The factors that enhance the performance of the schemes are effective utilizable recharge rates, extent of surface irrigation, and aquifer storage space. The factors that adversely affect the performance are the extent of the population covered by groundwater-based schemes and irrigation water demand per unit area. Subsequently, the districts in Maharashtra where groundwater-based schemes are likely to succeed were identified. The article also explains the practical and policy relevance of the model results for rural water supply planning.
Helical structure of polypeptides from the c-terminal half of hiv-1 vpr
Authors: Yao Shenggen , Azad Ahmed A. , Macreadie Ian G. , Norton Raymond S. 
Published: November 2022

Abstract:
HIV-I viral protein R (Vpr), is a 96-residue protein with a number of functions, some of which have been localised to distinct domains in the sequence. This paper describes the solution conformation, determined by NMR, of synthetic peptides encompassing a putative transmembrane helical domain of Vpr associated with formation of cation-selective channels in lipid bilayers. Peptides Vpr50•75 (residues 50-75 of Vpr) and Vpr50"82
both formed a-helices, encompassing residues 53-74 and 53-78, respectively. Thus, Vpr can form a helix long enough to traverse a biological membrane. The helix has some similarities to bee venom melittin, which can also form ion channels.
A Proposed Model for The Late-Infantile Neuronal Ceroid Lipofuscinosis (Batten Disease) Protein Cln2
Authors: Wallace B.A. , Orry Andrew 
Published: November 2022

Abstract:
The CLN2 protein, associated with late-infantile neuronal ceroid lipofuscinosis (Batten disease), appears to be a classical anchored (one transmembrane segment) membrane protein. A model is proposed for its structure in membranes, and how it may function as a proteinase to aid in the maturation of subunit c of the mitochondrial ATP complex. Its role is contrasted with that of the CLN3 protein, which is involved in the juvenile form of the disease.
Jack Bean Seed Coat Contains a Protein with Complete Sequence Homology to Bovine Insulin
Authors: Oliveira Antonia Elenir A. , Machado Olga L. T. , Gomes Valdirene M. , Netot Jose Xavier , Pereirat Alexandre C. , Vieira H Jose Gilberto H. , Fernandes Katia V. S. , Xavier-Filho Jose 
Published: November 2022

Abstract:
The present study reports that a protein with complete sequence homology to bovine insulin is present in Jack bean (Canavalia ensiformis) seed coats. This protein was recognized by anti-human insulin antibodies and lowered blood glucose levels of alloxanized mice, indicating that it possesses biological potency. Our results suggest that insulin-like activities previously found in diverse plant tissues may be indeed due to insulin and indicate that insulin-dependent signaling pathways have been remarkably conserved during evolution.
Primary Structure and Kinetic Interaction with Glycoproteins of The Lectin From Seeds of Cratylia Flor/Bunda
Authors: S. Cavada Benildo , AP. Nogueira Nadia , FariasI Creuza M.SA , Grangeiro Thalles B. , Ramos Marcia V , Thole Hubert H. , Raida Manfred , Rouge Pierre , Calvete Juan J 
Published: November 2022

Abstract:
The complete 236-amino-acid sequence of the glucose/mannose specific lectin from seeds of Cratylia floribunda (CFL) was determined by automated Edman sequencing of overlapping proteolytic peptides purified by HPLC after digestion of the lectin with endoproteinases Lys-C, Asp-N, trypsin and chymotrypsin. Mass spectrometry confirmed the sequence analysis and showed that CFL consists of a mixture of full length, single­ chain polypeptide (a-chain.-25397 ± 3 Da) and its• noncovalently associated p (residues 1-11 , 12847 ± 2 Da)
and y (residues 119-236, 12568 ± 1 Da) fragments. The primary structure of Cratylia floribunda lectin has extensive amino acid sequence homology with those of lectins from species of the taxonomically related genera Canavalia and Dioclea. However, using surface plasmon resonance, CFL and ConA, the seed lectin from Canavalia ensiformis, displayed distinct kinetic interactions with glycoproteins, indicating structural differences in their extended glycan binding-sites.
Enzymatic Degradation of Nociceptin Studied by LC-MS
Authors: J. Silherring , M.T. Smoluch , P. Suder , J. Kotlinska , M. Sallberg 
Published: November 2022

Abstract:
The fate of nociceptin was investigated, using size exclusion chromatography linked to the electrospray ionization mass spectrometry. Heptadecapeptide was processed to the major metabolites: nociceptin (1-11) and (1-6). The strategy described here and involving LC-MS using a size-exclusion chromatography is convenient and rapid and minimizes identification problems often connected to the analysis of complex mixtures.
Purification and Crystallization of a Protoca TechuaTe 4,5-Dioxygenase Sphingomonas Paucimobilis SYK-6.
Authors: Mitsui Yukio , Sugimoto Keisuke , Aoshima Hisae , Senda Toshiya , Masai Eiji , Fukuda Masao 
Published: November 2022

Abstract:
A protocatechuate 4,5-dioxygenase from Sphingomonas paucimobilis'SYK.-6 has been crystallized by hanging drop vapor-diffusion method. The crystals were grown from a solution containing ammonium sulfate
and Tris-HCI. The crystals belonged to the monoclinic system with a space group n and unit-cell dimensions
of a=65.4, b=66.5, c=l l9.8A and.,6=92.5°. The crystals diffract to at least 2.2A resolution.
The Roles of Natural Alkaloids and Polyphenols in Lipid Metabolism:
Therapeutic Implications and Potential Targets in Metabolic Diseases
Authors: Ma Zeqiang , Wang Shengnan , Miao Weiwei , Zhang Zhiwang , Yu Lin , Liu Siqi , Luo Zupeng , Liang Huanjie , Yu Jingsu , Huang Tengda , Li Mingming , Gao Jiayi , Su Songtao , Li Yixing , Zhou Lei 
Published: November 2022

Abstract:
The prevalence of obesity and its associated diseases has increased dramatically,
and they are major threats to human health worldwide. A variety of approaches, such
as physical training and drug therapy, can be used to reduce weight and reverse associated
diseases; however, the efficacy and the prognosis are often unsatisfactory. It has been
reported that natural food-based small molecules can prevent obesity and its associated
diseases. Among them, alkaloids and polyphenols have been demonstrated to regulate
lipid metabolism by enhancing energy metabolism, promoting lipid phagocytosis, inhibiting
adipocyte proliferation and differentiation, and enhancing the intestinal microbial
community to alleviate obesity. This review summarizes the regulatory mechanisms and
metabolic pathways of these natural small molecules and reveals that the binding targets
of most of these molecules are still undefined, which limits the study of their regulatory
mechanisms and prevents their further application. In this review, we describe the use of
Discovery Studio for the reverse docking of related small molecules and provide new insights
for target protein prediction, scaffold hopping, and mechanistic studies in the future.
These studies will provide a theoretical basis for the modernization of anti-obesity
drugs and promote the discovery of novel drugs.
Protein Informatics and Vaccine Development: Cancer Case Study
Authors: Verma Saroj , Masand Neeraj , Cheke Rameshwar S. , Patil Vaishali M. 
Published: November 2022

Abstract:
Clinical translation is a challenging step in the development of cancer vaccines and is found to be related to the complex nature of cancer immunology. Vaccine-based therapeutic strategies for cancer have gained consideration with the advent of vaccine technology as well as an understanding of cancer immunology. Immunotherapy has been widely used in the treatment of cancer. Some promising candidates have been identified to engineer cancer vaccines like Glycoprotein, Mucin 1, MHC protein, etc. It has benefited from the availability of advanced techniques for rapid identification and selection of proteins for precision engineering. Simultaneously, nanovaccines have been focused on target delivery and artificial intelligence-based approaches for personalized vaccine development. The manuscript summarizes the advances in the development of structure-based cancer vaccines along with the status of clinical studies and applications.
Folic Acid Promoted the Coupling Reaction of Epoxides and CO2
Authors: Chai Mengliang , Wu Fengtian , Wu Ling 
Published: November 2022

Abstract:
The process of hydrogen bond donor accelerating the cycloaddition of epoxides with CO2
is green access to high economic value cyclocarbonate derivatives. However, hydrogen bond donor
still has certain limitations such as poor biocompatibility and narrow substrate scope. Our group found
that folic acid could promote the coupling reaction of epoxides and CO2 through hydrogen-bonding.
The reaction was used to synthesize various cyclocarbonate derivatives in good to high yields with the
aid of folic acid and TBAB. In addition, benzoic acids and 2,4-quinazoline dione were synthesized in
the presence of CuCl2/folic acid and PdCl2/folic acid, respectively. The reaction mechanism was proposed
based on previous reports and control experiments.
Syringin as TGF-βR1, HER2, EGFR, FGFR4 Kinase, and MMP-2
Inhibitor and Potential Cytotoxic Agent against ER+ Breast Cancer Cells
Authors: Vasquez Ross D. , Aventurado Charlaine A. , Castillo Agnes L. 
Published: November 2022

Background:
Breast cancer is currently the most diagnosed cancer worldwide. Neoplastic
cells and components of the tumor microenvironment trigger enzymes and receptors to facilitate
cancer advancement. Syringin, a natural phenylpropanoid glycoside, has been reported to
possess anti-cancer activity and affinity with numerous druggable targets of breast carcinoma.

Objectives:
This work aims to evaluate the effects of syringin on the growth of breast cancer cells
(MCF-7) and normal dermal fibroblast cells (HDFn) and its ability to inhibit the protein targets of
breast cancer.

Methods:
Syringin was investigated on cell lines in vitro via MTT assay. Using non-cell-based activity
assay kits, its influence on the activity of transforming growth factor-beta receptor type 1
(TGF-βR1), human epidermal growth factor receptor (HER2), epidermal growth factor receptor
(EGFR), fibroblast growth factor receptor 4 (FGFR4), and matrix metalloproteinase-2 (MMP-2)
was evaluated.

Results:
Syringin exhibited significant cytotoxicity against MCF-7 cells (IC50: 32.11 μM for 24
hours and 21.35 μM for 48 hours) and was non-toxic on healthy HDFn cells (IC50: >100 μM for 24
and 48 hours). It significantly suppressed the activity of cancer and angiogenesis regulating enzymes
in vitro with commendable IC50 values on TGF-βR1 kinase (IC50: 6.48 μM), HER2 kinase
(IC50: 7.18 μM), EGFR kinase (IC50: 12.38 μM), FGFR4 kinase (IC50: 16.03 μM), and MMP-2
(IC50: 16.07 μM).

Conclusion:
Findings showed the selective toxicity of syringin on breast cancer cells and its potential
against pro-angiogenic enzymes. These discoveries strongly indicate the significance and
therapeutic potential of syringin in targeted cancer therapy.
Research and Patents Status of Selected Phytochemicals Against Cancer:
How Close and How Far?
Authors: Fatma Homa , Siddique Hifzur R 
Published: November 2022

Background:
Cancer is a global health issue and economic burden with a continuous
increase in incidence and mortality. Over the years, the underlying molecular mechanism of cancers
was thoroughly researched, leading to multiple drugs' development. Unfortunately, most
drugs have some serious drawbacks, such as therapy resistance and toxicity. Epidemiological studies
have shown that a diet rich in fruits and vegetables has cancer prevention properties, which
shifted the attention to the potential role of phytochemicals in anti-carcinogenic activity.

Objective:
To review the present status of phytochemicals research and patents in cancer prevention
and chemosensitization.

Methods:
We explored the relevant published articles and patents to review the phytochemicals
showing cancer preventive role in preclinical settings from 1997 onwards.

Results:
We summarise the role of phytochemicals on anti-carcinogenic, anti-inflammatory, antiproliferative,
anti-metastatic, and pro-apoptotic activities in both in vitro and in vivo. Thus, phytochemicals
might be an excellent chemosensitizing agent against chemoresistant cells and possibly
one of the safest and most effective options for cancer therapy. However, one of the limitations of
phytochemicals is their poor bioavailability and rapid excretion. Several analogs have been introduced
to increase bioavailability, better biological efficacy, absorption, and retention. In fact, various
phytochemicals and their analogs have been patented for their anti-cancerous properties.

Conclusion:
This mini-review discusses various phytochemicals and their anti-cancerous and
chemosensitizing roles. Due to their clinical relevance, recent trends in phytochemical extraction
and exploration have shown that more and more phytochemicals are being patented.
Natural Bioactive Compounds against Oxidative Stress: Dietary Polyphenols
Strike Back
Authors: Arrigoni Roberto , Cammarota Francesco , Porro Rosa , Cantore Stefania , Dioguardi Mario , Cazzolla Angela Pia , De Leonardis Francesco , Polimeno Lorenzo , Zerman Nicoletta , Di Cosola Michele , Mastrangelo Filiberto , Santacroce Luigi , Ballini Andrea 
Published: November 2022

Abstract:
Oxidative stress is a major cellular and metabolic burden that can really alter cell life
and become the base for disease onset and development. Many widespread pathologies can develop
from an unresolved oxidative stress situation; thus, addressing this state is paramount for
human health. Our antioxidant enzymes sometimes are not just enough. Fortifying our defense
and the antioxidant and anti-inflammatory system can make a difference in our health: if this is
attainable with our dietary habits, it could be a dream come true. Polyphenols are a fantastic tool
indeed in the fight against oxidative stress: they are easy to obtain, with little cost, no side effects,
and have a multitude of metabolic actions. This perspective review would shed light on polyphenol’s
metabolic and molecular action regarding oxidative stress to help preserve our health.
Information Consumption During Covid – 19
Authors: Alomiry Helial 
Published: November 2022

Background:
The Coronavirus disease (COVID-19) was declared a global pandemic in March 2020, only two months after its discovery in Wuhan. This pervasiveness and the epidemic's detrimental effects have seen verified and unverified information avalanche which attempted to help prevent, control and define the disease.

Objectives:
The study focused on three objectives. First, it determines how consumption of information relating to coronavirus occurred, focusing on the type and nature of the information utilized and its rationale. Second, it examines the impact of information consumption on preventive practices. Third, it evaluates the effect of gender and age on the consumption of information relating to coronavirus.

Methods:
The study adopted a cross-sectional online survey based on quantitative methods. The study included 400 participants from various regions of the world. The data were then subjected to analysis using SPSS.

Results:
The research analysis has been shaped by Pearson’s Correlation, Coefficient, Percentage, and Frequency which have been used to derive the information consumption rate during the pandemic.

Conclusion:
Information consumption was influenced by variables such as age and gender. The participants below the age of 40 years used social media as the source of information.
Participants above the age of 40 years favored legacy media like print and television. The study also evaluated the use of the information and found that most people sought the information to come up with preventive measures to protect them against the disease.
Locust Bean Gum: Processing, Properties and Food Applications
Authors: Singh Arun Kumar , Malviya Rishabha , Rao Gudhanti Siva Naga Koteswara 
Published: November 2022

Abstract:
Locust bean gum is derived from the seed endosperm of the Ceratonia siliqua carob tree and is known as locust bean or carob gum. Food, medicines, paper, textile, oil drilling, and cosmetic sectors all use it as an ingredient. Hydrogen bonding with water molecules makes locust bean gum useful in industrial settings. In addition, its dietary fibre activity helps regulate numerous health issues, including diabetes, bowel motions, heart disease and colon cancer. Locust bean gum production, processing, composition, characteristics, culinary applications, and health advantages are the subject of this article.
Impact of Personalized Avatars and Motion Synchrony on Embodiment and Users’ Subjective Experience: Empirical Study
Authors: Jung Myeongul , Sim Sangyong , Kim Jejoong , Kim Kwanguk 
Published: November 2022

Background
Embodiment through a virtual avatar is a key element for people to feel that they are in the virtual world.

Objective
This study aimed to elucidate the interaction between 2 methods of eliciting embodiment through a virtual avatar: motion synchronization and appearance similarity between a human and avatar, to understand embodiment (agency, body ownership, and self-location) and subjective experience (presence, simulator sickness, and emotion) in virtual reality.

Methods
Using a full-body motion capture system, 24 participants experienced their virtual avatars with a 3D-scanned face and size-matched body from a first-person perspective. This study used a 2 (motion; sync and async) × 2 (appearance; personalized and generic) within-subject design.

Results
The results indicated that agency and body ownership increased when motion and appearance were matched, whereas self-location, presence, and emotion were affected by motion only. Interestingly, if the avatar’s appearance was similar to the participants (personalized avatar), they formed an agency toward the avatar’s motion that was not performed by themselves.

Conclusions
Our findings would be applicable in the field of behavioral therapy, rehabilitation, and entertainment applications, by eliciting higher agency with a personalized avatar.