bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Variable-Length B-Cell Epitopes for Antipeptide Paratopes
Using the Program HAPTIC
Authors: Caoili Salvador E.C. 
Published: February 2022

Background:
Background: B-cell epitope prediction for antipeptide antibody responses enables peptide-based vaccine design and related translational applications. This entails estimating epitope-paratope binding free-energy changes from antigen sequence; but attempts to do so assuming uniform epitope length (e.g., of hexapeptide sequences, each spanning a typical paratope diameter when fully extended) have neglected empirically established variation in epitope length.

Objective:
Objective: This work aimed to develop a sequence-based physicochemical approach to variable-length B-cell epitope prediction for antipeptide paratopes recognizing flexibly disordered targets.

Method:
Method: Said approach was developed by analogy between epitope-paratope binding and protein folding modeled as polymer collapse, treating paratope structure implicitly. Epitope-paratope binding was thus conceptually resolved into processes of epitope compaction, collapse and contact, with epitope collapse presenting the main entropic barrier limiting epitope length among non-polyproline sequences. The resulting algorithm was implemented as a computer program, namely the Heuristic Affinity Prediction Tool for Immune Complexes (HAPTIC), which is freely accessible via an online interface (http://badong.freeshell.org/haptic.htm). This was used in conjunction with published data on representative known peptide immunogens

Results:
Results: HAPTIC predicted immunodominant epitope sequences with lengths limited by penalties for both compaction and collapse, consistent with known paratope-bound structures of flexibly disordered epitopes. In most cases, the predicted association constant was greater than its experimentally determined counterpart but below the predicted upper bound for affinity maturation in vivo.

Conclusion:
Conclusion: HAPTIC provides a physicochemically plausible means for estimating the affinity of antipeptide paratopes for sterically accessible and flexibly disordered peptidic antigen sequences, by explicitly considering candidate B-cell epitopes of variable length
Structural and Binding Properties of the Active Cell Wall Hydrolase
RipA from M. tuberculosis, a Promising Biosensing Molecule for Early
Warning Bacterial Detection
Authors: Squeglia Flavia , Marasco Daniela , Ruggiero Alessia , Testa Genni , Esposito Luciana , Berisio Rita 
Published: February 2022

Background:
Peptidoglycan is an essential component of the cell wall in all
bacteria. In particular, the cell walls of Gram-positive bacteria are composed mostly of a
thick layer of peptidoglycan. Its accessibility has important implications for their sensing
in whole bacterial detection methodologies. Indeed, there is an urgent demand for rapid
tests which can identify whole bacteria, e.g., directly at the point of care.

Objective:
The aim of this work is to explore the suitability of RipA, a key cell division
protein of M. tuberculosis, for whole cell biosensing of Gram-positive bacteria.

Methods:
We here conducted Molecular Dynamics (MD) studies aimed at the understanding
of the structural and dynamic features of active RipA and at the design of a suitable
bioreceptor. Based on these studies, we engineered a RipA variant for covalent oriented
immobilisation on golden surfaces and are able to bind peptidoglycan, albeit without
degrading it. Surface Plasmon Resonance (SPR) was employed to check the ability of
functionalized golden chips to recognize whole bacteria.

Results:
MD analyses elucidated the structural details of the active form of RipA and
suggested that this enzyme, once inactivated, presents a rigid and well-exposed peptidoglycan
recognition cleft. We engineered RipA for proper oriented immobilisation on golden
chips for SPR studies. Results show that once chemically coupled to a golden chip,
the developed RipA-based bioreceptor is able to detect B. subtilis, used as a model in a
concentration-dependent mode.

Conclusion:
Results highlight the potential of the engineered molecule to be integrated
in the development of early warning biosensors for Gram-positive contamination in clinical
diagnosis or food-borne infections.
An Unfolded Protein Response-Related mRNA Signature Predicting the
Survival and Therapeutic Effect of Hepatocellular Carcinoma
Authors: Chen Gang , Wu Junxin , Su Zhixiong , Wang Lei , Chen Xingte , Zhong Xiaohong , Wang Di , Wang Jianchao , Shao Lingdong 
Published: February 2022

Background:
Tumorigenesis, metastasis, and treatment response of hepatocellular carcinoma
(HCC) are regulated by unfolded protein responses (UPR) signaling pathways, including
IRE1a, PERK, and ATF6, but little is known about UPR related genes with HCC prognosis and
therapeutic indicators.

Objective:
We aimed to identify a UPR related prognostic signature (UPRRPS) for HCC and explore
the potential effect of the current signature on the existing molecular targeted agents and immune
checkpoint inhibitors (ICIs).

Methods:
We used The Cancer Genome Atlas (TCGA) database to screen candidate UPR genes
(UPRGs), which are expressed differentially between hepatocellular carcinoma and normal liver
tissue and associated with prognosis. A gene risk score for overall survival prediction was established
using the least absolute shrinkage and selection operator (LASSO) regression analysis,
which was validated using data from the International Cancer Genome Consortium (ICGC) database
and evaluated by the C-index. Then immune and molecular characteristics stratified by the
current UPRRPS were analyzed, and the corresponding drug sensitivity was conducted.

Results:
Initially, 42 UPRGs from the TCGA database were screened as differentially expressed
genes, which were also associated with HCC prognosis. Using the LASSO regression analysis,
nine UPRGs (EXTL3, PPP2R5B, ZBTB17, EIF2S2, EIF2S3, HDGF, SRPRB, EXTL2, and TPP1)
were used to develop a UPRRPS to predict the OS of HCC patients in the TCGA set with the Cindex
of 0.763. The current UPRRPS was also well-validated in the ICGC set with the C-index of
0.700. Multivariate Cox regression analyses also confirmed that the risk score was an independent
risk factor for HCC in both the TCGA and ICGC sets (both P<0.05). Functional analyses showed
that low-risk score was associated with increased natural killer cells, T helpers, tumor immune dysfunction
and exclusion score, microsatellite instability expression, and more benefit from ICIs; the
high-risk score was associated with increased active dendritic cells, Tregs, T-cell exclusion score,
and less benefit from ICIs. Gene set enrichment analyses showed that the signaling pathways of
VEGF, MAPK, and mTOR were enriched in high UPRRPS, and the drug sensitivities of the corresponding
inhibitors were all significantly higher in the high UPRRPS subgroup (all P<0.001).

Conclusion:
With the current findings, UPRRPS was a promising biomarker for predicting the
prognosis of HCC patients. UPRRPS might also be taken as a potential indicator to guide the management
of immune checkpoint inhibitors and molecular targeted agents.
Comparative Transcriptome Analysis of Flower Senescence of Camellia
lutchuensis
Authors: Liu Weixin , Yin Hengfu , Feng Yi , Yu Suhang , Fan Zhengqi , Li Xinlei , Li Jiyuan 
Published: February 2022

Background:
Background: Flower senescence is the last stage of flower development and affects the ornamental and economic value of flower plants. There is still less known on flower senescence of the ornamental plant Camellia lutchuensis, a precious species of Camellia with significant commercial application value.

Methods:
Methods: Transcriptome sequencing was used to investigate the : By Illumina HiSeq sequencing, we generated approximately 101.16 Gb clean data and 46649 differentially expressed unigenes. Based on the different expression pattern, differentially expressed unigenes were classified into 10 Sub Class. And Sub Class 9, included 8252 unigenes, was highly expressed in the flower senescent stage, suggesting it had a potential regulatory relationship of flower senescence. First, we found that ethylene biosynthesis genes ACSs, ACOs, receptor ETR genes and signaling genes EINs, ERFs all upregulated during flower senescence, suggesting ethylene might play a key role in flower senescence of C. lutchuensis. Furthermore, reactive oxygen species (ROS) production related genes peroxidase (POD), lipase (LIP), polyphenoloxidase (PPO), and ROS scavenging related genes glutathione S-transferase (GST), glutathione reductase (GR) and superoxide dismutase (SOD) were induced in senescent stage, suggesting ROS might be involved in the flower senescence. Besides, the expression of monoterpenoid and isoflavonoid biosynthesis genes, transcription factors (WRKY, NAC, MYB and C2H2), senescence-associated gene SAG20 also were increased during flower senescence.

Conclusion:
Conclusion: In C. lutchuensis, ethylene pathway might be the key to regulate flower senescence, and ROS signal might play a role in the flower senescence.
A Combinational Approach for More Efficient miRNA Biosensing
Authors: Lee Cheolho 
Published: February 2022

Abstract:
A microRNAs, short single-stranded noncoding RNAs ranging in length from 18 ~ 24 bp, are found in all kingdoms of eukaryotes and even viruses. It was found that miRNAs got involved in a variety of biological phenomenon control and their intracellular aberrant expression was related to diseases and abnormalities in the immune system. Since then, it has been considered essential to develop an efficient miRNA detection system. In this review, the limitations of traditional scheme-based miRNA detection methods are compared and analyzed. In particular, nucleic acid amplification based miRNA detection methods and nanomaterial-based miRNA detection methods, which are widely used as a biosensing platform because of such features and advantages as high sensitivity, specificity, and simplicity were analyzed. Based on this analysis, the latest examples of combination of advantages of nucleic acid amplification and the features and advantages of nanomaterials are examined to suggest the characteristics of the next generation of miRNA biosensing.
An Insight into the Molecular Mechanism of Mitochondrial Toxicant-induced Neuronal Apoptosis in Parkinson’s Disease
Authors: Calivarathan Latchoumycandane , Brahadeeswaran Subhashini , Lateef Mohammad 
Published: February 2022

Abstract:Parkinson’s disease (PD) is one of the most common progressive neurodegenerative disorders affecting approximately 1% of the world’s population at the age of 50 and above. Majority of PD cases are sporadic and show symptoms after the age of 60 and above. At that time, most of the dopaminergic neurons in the region of substantia nigra pars compacta have been degenerated. Although in past decades, discoveries of genetic mutations linked to PD have significantly impacted our current understanding of the pathogenesis of this devastating disorder, it is likely that the environment also plays a critical role in the etiology of sporadic PD. Recent epidemiological and experimental studies indicate that exposure to environmental agents, including a number of agricultural and industrial chemicals, may contribute to the pathogenesis of several neurodegenerative disorders, including PD. Furthermore, there is a strong correlation between mitochondrial dysfunction and several forms of neurodegenerative disorders, including Alzheimer’s disease (AD), Huntington’s disease (HD), Amyotrophic lateral sclerosis (ALS) and PD. Interestingly, substantia nigra of patients with PD has been shown to have a mild deficiency in mitochondrial respiratory electron transport chain NADH dehydrogenase (Complex I) activity. This review discusses the role of mitochondrial toxicants in the selective degeneration of dopaminergic neurons targeting the electron transport system that leads to Parkinsonism.
Proteomic Profile Analysis of Pulmonary Artery in a Rat Model Under
Hypoxic Pulmonary Hypertension
Authors: Yan Ma , Shuang Ma , Jie Liu , Ruixia Zhang , Chuanchuan Liu 
Published: February 2022

Aim:
Proteomic profile analysis of pulmonary artery in a rat model under hypoxic pulmonary hypertension

Background:
Background:	Hypoxic pulmonary hypertension (HPH) is a pathological condition exemplified by a constant rise in pulmonary artery pressure in high-altitudes.

Objective:
Objective: To investigated the proteome profile and response mechanisms of SD rats under hypoxia over a period of four-weeks.

Method:
Method: Proteomic profile analysis of pulmonary artery in a rat model under hypoxic pulmonary hypertension.

Results:
Results: With 3,204 proteins identified, 49 were up-regulated while 46 were down-regulated. Upregulated genes included Prolargin, Protein S100-A6 and Transgelin-2, whereas Nascent polypeptide-associated complex and Elongator complex protein 1 were down-regulated. KEGG enriched pathways had purine metabolism, cancer and lipolysis regulation as significantly enriched in hypoxic group.

Conclusion:
Conclusion: In conclusion, our findings submit basis for downstream studies on tissue hypoxia mechanisms alongside the associated physiological conditions.
Hypoxic pulmonary hypertension (HPH) is a pathological condition exemplified by a constant rise in pulmonary artery pressure in high altitudes. Herein, we investigated the proteome profile and response mechanisms of Sprague-Dawley (SD) rats under hypoxia over a period of four weeks. Unbiased iTRAQ-based quantitative proteomics was utilized in proteome profile analysis of a rat model exposed to HPH. With 3,204 proteins identified, 49 were upregulated while 46 were downregulated. Upregulated genes included Prolargin, Protein, S100-A6 and Transgelin-2, whereas Nascent polypeptide-associated complex and Elongator complex protein 1 were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched pathways had purine metabolism, cancer, and lipolysis regulation as significantly enriched in hypoxic group. In conclusion, the findings from this study submit a basis for downstream studies on tissue hypoxia mechanisms alongside the associated physiological conditions.
Recent Advances in Drug Design and Delivery Across Biological Barriers
Using Computational Models
Authors: Vanshita  , Garg Akash , Dewangan Hitesh Kumar 
Published: February 2022

Abstract:
The systemic delivery of pharmacological substances generally exhibits several significant
limitations associated with the bio-distribution of active drugs in the body. Human body’s defense mechanisms
have been found to become impediments to drug delivery. Various technologies have evolved to
overcome these limitations, including computational approaches and advanced drug delivery. As the body
of a human has evolved to defend itself from hostile biological as well as chemical invaders, the biological
barriers, such as ocular barriers, blood-brain barriers, intestinal and skin barriers, also limit the passage
of drugs across desired sites. Therefore, efficient delivery remains an utmost challenge for researchers
and scientists. The present review focuses on the techniques to deliver the drugs with efficient therapeutic
efficacy at the targeted sites. This review article provides an insight into the main biological barriers
along with the application of computational or numerical methods to deal with different barriers by
determining the drug flow, temperature and various other parameters. It also summarizes the advanced
implantable drug delivery systems to circumvent the inherent resistance exhibited by these biological
barriers, and in turn, to improve the drug delivery process.
Necrotizing Enterocolitis: Clinical Features, Histopathological Characteristics,
and Genetic Associations
Authors: Maheshwari Akhil , Traub Terri M. , Garg Parvesh M. , Ethawi Yahya , Buonocore Giuseppe 
Published: February 2022

Abstract:
Necrotizing enterocolitis (NEC) is an inflammatory bowel necrosis seen in premature in-fants. Although the etiopathogenesis of NEC is unclear, genetic factors may alter a patient's suscepti-bility, clinical course, and outcomes. This review draws from existing studies focused on individual genes and others based on microarray-based high-throughput discovery techniques. We have included evidence from our own studies and from an extensive literature search in the databases PubMed, EMBASE, and Scopus. To avoid bias in the identification of studies, keywords were short-listed a priori from anecdotal experience and PubMed’s Medical Subject Heading (MeSH) thesaurus.
Chronic Kidney Disease, Metabolic Syndrome, and Cardiovascular Risk: Insights and Associated Mechanistic Pathways
Authors: Nogueira Thaís Rodrigues , Marreiros Camila Santos , de Jesus e Silva de Almendra Freitas Betânia 
Published: February 2022

Abstract:
This study is a narrative review that aims to address the conceptual, characteristic, pathophysiological, and mechanistic aspects that define the profile of metabolic syndrome and chronic kidney disease. The objective was to investigate current knowledge and elucidate, through discussions on the topic, the main interrelated paths. This review was carried out unsystematically, from March to May 2020, by means of a survey of the literature indexed in the PubMed, Web of Science, and Scopus (Elsevier®) databases. The scientific materials collected showed that the cross-talk between the diseases in question is mainly based on the conditions of resistance to insulin action, endothelial dysfunction, activation pathways of the Renin-Angiotensin-Aldosterone system and adipokine imbalance, also emphasizing the influence of atherosclerotic events in kidney damage. Furthermore, it was reinforced the fact that inflammatory processes play an important role in the worsening and evolution of the clinical condition of patients, especially when they have underlying pathologies chronically treated for subclinical inflammation. It is expected that a greater number of original researches will propose to investigate other possible interactions, with a view to standardized treatment of these diseases or nutritional management.
Clinical Overview of Arthritis with a Focus on Management Options and Preventive Lifestyle Measures for its Control
Authors: Gupta Umesh Chandra , Gupta Subhas Chandra , Gupta Saira Sugandh 
Published: February 2022

ABSTRACT:Arthritis is the spectrum of conditions that cause swelling and tenderness of one or more body joints with key symptoms of joint pain and stiffness. Its progression is closely linked to age. Although there are a number of arthritis types, such as ankylosing, gout, joint infections, juvenile idiopathic, reactive, and septic, the two most common types are osteoarthritis and rheumatoid arthritis. Osteoarthritis causes the articulating smooth cartilage that covers the ends of bones, forming a joint, to break down. Rheumatoid arthritis is a disease in which the immune system attacks joints, beginning with the cartilaginous lining of the joints. The latter is considered a systemic disease, i.e., affecting many parts of the body, but the respiratory system is involved in 10 to 20% of all mortality. Osteoarthritis is one of the leading causes of disability globally. Several preventive measures to control arthritis have been suggested, such as using analgesics, non-steroid anti-inflammatory drugs, moderate to vigorous physical activity and exercise, reducing sedentary hours, getting adequate sleep, and maintaining healthy body weight. Foods including a Mediterranean diet rich in fruits and vegetables, fish oil, medicinal plants, and microbiota are vital protective methods. The intake of vitamins, such as A and C, minerals, e.g., selenium and zinc, polyunsaturated and n-3 fatty acids, is also a significant preventive measure.
Efficacy of Regenerative Medicine for Alveolar Cleft Reconstruction: A
Systematic Review and Meta-analysis
Authors: Motamedian Saeed Reza , Mohaghegh Sadra , Lakmazaheri Ehsan , Ahmadi Nima , Kouhestani Farnaz 
Published: February 2022

Objective:
The objective of this study is to analyze the efficacy and complications of regenerative
medicine compared to autogenous bone graft for alveolar cleft reconstruction.

Method:
Electronic search was done through PubMed, Scopus, Embase and Cochrane databases for the
studies published until May 2021. No limitations were considered for the type of the included studies. The
risk of bias (ROB) of the studies was assessed using the Cochrane Collaborations and NIH quality assessment
tool. Meta-analyses were performed to assess the difference in the amount of bone formation
and rate of complications. Grading of Recommendations, Assessment, Development and Evaluation
(GRADE) was used for analyzing the level of the evidence.

Results:
Among a total of 42 included studies, 21 studies used growth factors, 16 studies delivered cells,
and five studies used biomaterials for bone regeneration of the alveolar cleft. Results showed no significant
difference in the amount of bone formation between bone morphogenic protein-2 and iliac graft
treated patients after six months (P = 0.44) and 12 months (P = 0.17) follow-up. Besides, higher swelling
(OR=9.46, P <0.01) and less infection (OR=0.19, P = 0.01) were observed in BMP treated patients. Using
stem cells can reduce the post-treatment pain (OR=0.04, P = 0.01), but it has no significant impact on
other complications (P > 0.05). Using tissue engineering methods reduced the operation time (SD=1.06,
P < 0.01). GRADE assessment showed that results regarding the amount of bone formation volume after
six and 12 months have low level of evidence.

Conclusion:
Tissue engineering methods can provide a comparable amount of bone formation to the autogenous
graft and reduce some of the complications, operation time and hospitalization duration.
Passive Solar-driven Interfacial Evaporation Nanosystems: Beyond Desalination
Towards Multiple Applications
Authors: Sheng Minhao , Bin Xiaoqing , Yang Yawei , Que Wenxiu 
Published: February 2022

Abstract:
Recently, passive solar-driven interfacial evaporation has become one of the fastest-growing
technologies for solar energy utilization and desalination. Herein, we provide an overview of other
emerging and potential applications of evaporation nanosystems beyond desalination, i.e., electricity
generation, organics rejection, and sterilization. These extended functions can be a benefit for energy
and environmental issues.