syedzayyan/paper_mill_benchmark huggingface dataset:
Recent Advances of Organ-on-a-Chip in Cancer Modeling Research.

Although many studies have focused on oncology and therapeutics in cancer, cancer remains one of the leading causes of death worldwide.Due to the unclear molecular mechanism and complex in vivo microenvironment of tumors, it is challenging to reveal the nature of cancer and develop effective therapeutics.Therefore, the development of new methods to explore the role of heterogeneous tme in individual patients' cancer drug response is urgently needed and critical for the effective therapeutic management of cancer.The organ-on-chip (oo c) platform, which integrates the technology of 3d cell culture, tissue engineering, and microfluidics, is emerging as a new method to simulate the critical structures of the in vivo tumor microenvironment and functional characteristics.It overcomes the failure of traditional 2d/3d cell culture models and preclinical animal models to completely replicate the complex tme of human tumors.As a brand-new technology, oo c is of great significance for the realization of personalized treatment and the development of new drugs.This review discusses the recent advances of oo c in cancer biology studies.It focuses on the design principles of oo c devices and associated applications in cancer modeling.The challenges for the future development of this field are also summarized in this review.This review displays the broad applications of oo c technique and has reference value for oncology development.

Journal: Biosensors (2022)
Publication types: Journal Article;Review
MICAL1 facilitates pancreatic cancer proliferation, migration, and invasion by activating WNT/β-catenin pathway.

Mical1 is involved in the malignant processes of several types of cancer; however, the role of mical1 in pancreatic cancer (pc) has not been well-characterized.This study aimed to investigate the expression and function of mical1 in pc.Methods rt-q pcr and immunohistochemistry were used to detect mical1 expression in pc and adjacent nontumor tissues.Cell counting kit-8, ed u, clone formation, wound healing, and transwell assays as well as animal models were used to investigate the effects of overexpression or inhibition of mical1 expression on the proliferation, invasion, and metastasis of pc cells.Rna-seq was used to explore the main pathway underlying the functions of mical1.Proteomics, mass spectrometry, and co-immunoprecipitation assays were used to investigate the interaction of proteins with mical1.Rescue experiments were conducted to validate these findings.Results both mical1 m rna and protein levels were upregulated in pc tissues compared with matched adjacent nontumor tissues.The expression level of mical1 was associated with the proliferative and metastatic status of pc.Repression of mical1 significantly inhibited pc cell growth, migration, and invasion in vitro and in vivo.Rna sequencing analysis indicated that mical1 was closely correlated with the wnt pathway.Overexpression of mical1 (1) promoted the phosphorylation of tbc1d1 at the ser660 site, (2) facilitated the distribution of fzd7 on the cytomembrane, (3) inhibited the degradation of fzd7 in the lysosome, and (4) activated the wnt pathway.Conclusions mical1 was upregulated in pc and involved in stimulating the progression of pc cells by activating the wnt/β-catenin signaling pathway.Therefore, mical1 is a potential therapeutic target for pc.

Journal: Journal of translational medicine (2022)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
IFPA meeting 2016 workshop report II: Placental imaging, placenta and development of other organs, sexual dimorphism in placental function and trophoblast cell lines.

Workshops are an important part of the ifpa annual meeting as they allow for discussion of specialized topics.At ifpa meeting 2016 there were twelve themed workshops, four of which are summarized in this report.These workshops addressed challenges, strengths and limitations of techniques and model systems for studying the placenta, as well as future directions for the following areas of placental research: 1) placental imaging; 2) sexual dimorphism; 3) placenta and development of other organs; 4) trophoblast cell lines.

Journal: Placenta (2017)
Publication types: Journal Article;Review
Gap junction with MLO-A5 osteoblast-like cell line induces ALP and BSP transcription of 3T3-L1 pre-adipocyte like cell line via Hspb1 while retaining adipogenic differentiation ability.

In bone tissues, gap junctions form direct links between the cytoplasm of an osteocyte and another adjacent osteocyte or osteoblast, which underlie both bone formation and bone resorption.We have previously demonstrated that alkaline phosphatase (alp) and bone sialoprotein (bsp), which are osteoblast markers, were induced in mesenchymal stem cells (mscs) co-cultured with osteoblast-like cell line.However, the molecular mechanism of this process has not been fully addressed.Furthermore, few advances have been made toward elucidating the communication networks that link the status of committed cells such as (pre-) adipocytes that differentiated from mscs as well as osteoblasts.Therefore, the objective of the present study was to investigate the mechanism underlying the communication network between pre-adipocytes and osteoblasts.We evaluated the effect of co-culture with osteoblast on the cell status of pre-adipocytes using murine osteoblast-like cell line, mlo-a5, and pre-adipocyte-like cell line, 3t3-l1, respectively.The results presented here demonstrated that osteoblasts and pre-adipocytes communicate via gap junctions, and the ensuing drastic increase in alp and bsp transcription in co-cultured pre-adipocytes was induced, at least partly, via heat shock protein family b member 1 (hspb1).In addition, terminal differentiation into adipocytes was suppressed in pre-adipocytes during co-culture with osteoblast without loss of adipogenic differentiation ability.Interestingly, after co-culture with osteoblasts, isolated co-cultured pre-adipocytes were able to differentiate to adipocytes as well as original pre-adipocytes.These results suggest that gap junctional communication with osteoblasts suppressed adipogenic differentiation of pre-adipocytes without loss of adipogenic differentiation ability.

Journal: Bone (2020)
Publication types: Journal Article;Research Support, Non-U.S. Gov't
High-resolution mass spectrometry exhalome profiling with a modified direct analysis in real time ion source.

Rationale exhaled breath contains many substances that are closely related to human metabolism.Analysis of its composition is important for human health, but it is difficult.Since the volatile molecules in breath samples are exhaled instantaneously, easily diffused and modified, and at low level of presence, they are difficult to identify and quantify.Methods a modified direct analysis in real time ion source was used for high-resolution mass spectrometry measurement of human metabolites in exhaled breath through online monitoring and offline analysis, in both positive and negative ion modes.The improved system enabled the breath volatiles as well as condensates to be directly sampled, rapidly transmitted and efficiently ionized in a confined region, and then detected using an orbitrap mass analyzer.Results the molecular features with online and offline analysis of exhaled breath were demonstrated with obvious differences.A total of about 65 metabolites in positive ion mode and about 55 metabolites in negative ion mode were identified based on accurate m/z values.Exhalome profile and the composition proportion of different classes of compounds were obtained.The relative contents of metabolites from breath varied during different time periods throughout a day.Conclusions a more complete picture of the human breath metabolome was provided combining the results obtained from both online and offline analysis.The developed method allows analysis of breath samples with different status rapidly and directly, and it features simple operation and metabolite identification, requiring little or no sample preparation.

Journal: Rapid communications in mass spectrometry : RCM (2022)
Publication types: Journal Article
A detailed electrochemical impedance spectroscopy study of a bismuth-film glassy carbon electrode for trace metal analysis.

A systematic electrochemical impedance spectroscopy (eis) analysis at different potentials of an in situ-prepared bismuth-film glassy carbon electrode (bi fe) in 0.1 m acetate buffer solution is reported.This electrode is employed in the square-wave anodic stripping voltammetry (swasv) technique for the determination of trace amounts of the heavy metals zn, cd, and pb.The method was first validated for detection limit, linear range, sensitivity, precision and accuracy to clearly prove the superior action of bi fe compared with the bare glassy carbon electrode (gce).Next, in order to investigate the characteristics of this sensor, eis measurements were carried out at slightly more negative potentials than the potentials at which each individual stripping signal is detected, after the deposition step at different deposition potentials.For comparison, eis measurements were also performed at open circuit potential.The studied trace metal concentration range (5-20 ppb) did not significantly influence the capacitive and resistive behaviour of the bi fe which explains why the performance of this sensor is superior compared with the bare gce.The higher sensitivity of the swasv method for bi fe compared with the bare gce was explained by the lower polarisation resistance values of the former.Moreover, the potential of zero charge was also determined, and an explanation whether the system is under kinetic- and/or diffusion-controlled process is given.

Journal: Analytica chimica acta (2018)
Publication types: Journal Article
Neurobiological underpinnings of emotions.

Emotion is a stirred-up state caused by physiological changes occurring as a response to some event and which tends to maintain or abolish the causative event.Understanding the neuroanatomical basis of the genesis and control of emotions is quintessential in understanding how biology affects the mind and in turn, helps in understanding our own nature.We present a short communication explaining the neurological basis of emotions.

Journal: Industrial psychiatry journal (2021)
Publication types: Journal Article
Coming in from the cold: overcoming the hostile immune microenvironment of medulloblastoma.

Medulloblastoma is an aggressive brain tumor that occurs predominantly in children.Despite intensive therapy, many patients die of the disease, and novel therapies are desperately needed.Although immunotherapy has shown promise in many cancers, the low mutational burden, limited infiltration of immune effector cells, and immune-suppressive microenvironment of medulloblastoma have led to the assumption that it is unlikely to respond to immunotherapy.However, emerging evidence is challenging this view.Here we review recent preclinical and clinical studies that have identified mechanisms of immune evasion in medulloblastoma, and highlight possible therapeutic interventions that may give new hope to medulloblastoma patients and their families.

Journal: Genes & development (2022)
Publication types: Journal Article;Review;Research Support, Non-U.S. Gov't;Research Support, N.I.H., Extramural
Photodynamic sensitizers modulate cytoskeleton structural dynamics in neuronal cells.

The neuronal cytoskeleton plays a crucial role in maintaining cell integrity and functioning of neurons.Cytoskeleton deformities have been reported to be associated with neurodegenerative diseases thus; cytoskeleton can be targeted for therapeutic strategies.The therapeutic application of photosensitive molecule is termed as photodynamic therapy (pdt).Pdt has been applied in the field of dermatology, cancer biology, and antimicrobial therapy.Pdt induces several changes in cells, which include induction of apoptosis, dna damage, and induction of inflammatory response.Pdt has been also reported to modulate cytoskeleton such as actin dynamics.The in vitro studies suggested that pdt using dyes such as toluidine blue and rose bengal effectively modulated the actin cytoskeleton, neurite outgrowth, tubulin, and tau aggregation.In this review, we focused on the effect of photosensitized molecules on various cytoskeleton proteins.We hypothesize that pdt could have potency against alzheimer's disease and other neurodegenerative disorders.

Journal: Cytoskeleton (Hoboken, N.J.) (2021)
Publication types: Journal Article;Research Support, Non-U.S. Gov't;Review
Pre-existing Vestibular Symptoms Are Associated With Acute Vestibular Symptoms After Gamma Knife Therapy for Vestibular Schwannoma.

To identify pretreatment variables associated with the development of acute vestibular symptoms after gamma knife (gk) treatment for vestibular schwannoma (vs).Study design retrospective case series.Setting tertiary neurotology referral center.Patients patients treated with gk radiosurgery for vs between march 2007 and march 2017 were considered for this study.Patients with neurofibromatosis type ii, previous vs surgery, follow-up less than 6 months, or the lack of t2 magnetic resonance imaging (mri) sequences from the day of treatment were excluded.Main outcome measures the presence of acute vestibular symptoms arising within 6 months after gk was the main outcome variable.Tumor, patient, and treatment characteristics were gathered from the medical record.Results in total, 98 patients met inclusion criteria.The incidence of acute vestibular symptoms occurring within 6 months after gk treatment was 46.9%.Post-gk vestibular symptoms were reported at a significantly higher frequency among subjects who had reported vestibular symptoms before their treatment (p = 0.001).Tumor size was not associated with a propensity to develop acute vestibular symptoms (p = 0.397).The likelihood of receiving a referral to vestibular rehabilitation services was not significantly different among patients with larger versus smaller tumor size, as defined by 1.6 cm and 1.4 cm thresholds (p = 0.896, p = 0.654).Conclusions inquiries aimed at revealing a history of vestibular complaints may prove useful in counseling patients on the likelihood of experiencing acute vestibular symptoms after treatment of vestibular schwannoma with gamma knife therapy.

Journal: Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology (2021)
Publication types: Journal Article
Macrophage polarization as a novel weapon in conditioning tumor microenvironment for bladder cancer: can we turn demons into gods?

Macrophages are major components of the immune infiltration in cancer where they can affect tumor behavior.In the bladder, they play important roles during the resolution of infectious processes and they have been associated with a worse clinical prognosis in bladder cancer.The present review focused on the characteristics of these important immune cells, not only eliciting an innate immune surveillance, but also on their importance during the cancer immunoediting process.We further discuss the potential of targeting macrophages for anticancer therapy, the current strategies and the state of the art as well as the foreseen role on combined therapies on the near future.This review shows how a comprehensive understanding of macrophages within the tumor should translate to better clinical outcome and new therapeutic strategies focusing especially on bladder cancer.

Journal: Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico (2019)
Publication types: Journal Article;Review
A glycine-functionalized graphene quantum dots synthesized by a facile post-modification strategy for a sensitive and selective fluorescence sensor of mercury ions.

In this work, we have developed a facile method for the synthesis of glycine-functionalized graphene quantum dots (gly-gqds) through post-modification of graphene quantum dots with gly under alkaline conditions.The as-synthesized gly-gqds exhibit an excellent blue emission at 444 nm, independent of excitation, as well as a high quantum yield (qy) of 35.7%.The gly-gqds have a narrow size distribution with an average size of 5.9 nm.Moreover, the as-prepared gly-gqds showed a better selective and sensitive recognition capability towards mercury ion (hg2+) in aqueous solutions with a low detection limit of 8.3 n m, compared with gqds and other nitrogen-doped gqds synthesized through the one-step solvent thermal method.Gly-gqds are successfully applied for the determination of hg2+in real water samples.This work shows a new promising approach for the design and synthesis of desirable gqds with a given function.

Journal: Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy (2021)
Publication types: Journal Article
Comparison of Bioorthogonal β-Lactone Activity-Based Probes for Selective Labeling of Penicillin-Binding Proteins.

Penicillin-binding proteins (pbps) are a family of bacterial enzymes that are key components of cell-wall biosynthesis and the target of β-lactam antibiotics.Most microbial pathogens contain multiple structurally homologous pbp isoforms, making it difficult to target individual pbps.To study the roles and regulation of specific pbp isoforms, a panel of bioorthogonal β-lactone probes was synthesized and compared.Fluorescent labeling confirmed selectivity, and pbps were selectively enriched from streptococcus pneumoniae lysates.Comparisons between fluorescent labeling of probes revealed that the accessibility of bioorthogonal reporter molecules to the bound probe in the native protein environment exerts a more significant effect on labeling intensity than the bioorthogonal reaction used, observations that are likely applicable beyond this class of probes or proteins.Selective, bioorthogonal activity-based probes for pbps will facilitate the activity-based determination of the roles and regulation of specific pbp isoforms, a key gap in knowledge that has yet to be filled.

Journal: Chembiochem : a European journal of chemical biology (2021)
Publication types: Comparative Study;Journal Article;Research Support, N.I.H., Extramural;Research Support, Non-U.S. Gov't
New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain.

Wrky transcription factors (tfs) constitute one of the largest families of plant tfs.Based on the organization of domains and motifs, wrky tfs are divided into three groups (i-iii).The wrky subgroup iia includes three representatives in a.Thaliana, at wrky18, at wrky40, and at wrky60, that participate in biotic and abiotic stress responses.Here we present crystal structures of the dna binding domain (dbd) of at wrky18 alone and in the complex with a dna duplex containing the wrky-recognition sequence, w-box.Subgroup iia wrky tfs are known to form homo and heterodimers.Our data suggest that the dimerization interface of the full-length at wrky18 involves contacts between the dbd subunits.Dna binding experiments and structural analysis point out novel aspects of dna recognition by wrky tfs.In particular, at wrky18-dbd preferentially binds an overlapping tandem of w-boxes accompanied by a quasi-w-box motif.The binding of dna deforms the b-type double helix, which suggests that the dna fragment must be prone to form a specific structure.This can explain why despite the short w-box consensus, wrky tfs can precisely control gene expression.Finally, this first experimental structure of a group ii wrky tf allowed us to compare group i-iii representatives.

Journal: International journal of biological macromolecules (2022)
Publication types: Journal Article
In utero exposure to LPS alters the postnatal acute-phase response in beef heifers.

The potential effect of prenatal lps exposure on the postnatal acute phase response (apr) to an lps challenge in heifers was determined.Pregnant crossbred cows were separated into prenatal immune stimulation (pis) and saline groups (control).From these treatments, heifer calves were identified at weaning to subsequently receive an exogenous lps challenge.Sickness behavior scores (sbs) were recorded and blood samples were collected at 30-min intervals from -2 to 8 h and again at 24 h relative to the lps challenge.There was a treatment × time interaction for the change in vaginal temperature (vt) such that the change in vt was greater in control than pis from 150 to 250 min, yet it was greater in pis than control from 355 to 440 min and from 570 to 1145 min.There was also a treatment × time interaction for sbs such that scores were greater in control than pis at 0.5 h, yet were greater in pis than control from 2.5 to 4 h post-lps.There was a tendency for a treatment × time interaction for serum concentrations of il-6, which were greater in pis than control heifers from 5.5 to 6 h and from 7 to 8 h post-challenge.Thus, a single exposure to lps during gestation can alter the postnatal apr to lps in heifer calves.

Journal: Innate immunity (2017)
Publication types: Journal Article
Agricultural Cold Chain Logistics Mode Based on Multi-Mode Blockchain Data Model.

Ing at the problem of massive data storage and transaction authority in the blockchain system in the data sharing transaction scenario, this paper proposes a blockchain system for the controllable sharing transaction of massive data.By designing the blockchain system model of the consortium chain and private chain, reconstructing the data structure of the block, and introducing the inter planetary file system (ipfs) technology, we adopt the off-chain storage method to solve the problem of high cost caused by too much data carried by the block.The isolation control of data resource transactions is realized by introducing identity authentication and channel mechanism, which meets the needs of different subjects for confidentiality of transaction data information.From the analysis results of cold chain logistics efficiency, in the five years from 2017 to 2021, the comprehensive cold chain logistics efficiency, pure technology cold chain logistics efficiency, and scale cold chain logistics efficiency of agricultural product cold chain logistics in a certain region have all reached above 0.9.The return to scale remains unchanged, and the cold chain logistics resources have been effectively allocated and reasonably utilized.The value of comprehensive cold chain logistics efficiency, pure technology cold chain logistics efficiency, and scale cold chain logistics efficiency in a certain month is less than 1, which means that the cold chain logistics efficiency is weak or ineffective.This shows that in these years, the infrastructure investment, cold chain technical support, and management level related to the cold chain logistics of agricultural products in a certain region need to be strengthened, and it is necessary to adjust the input-output structure and allocate resources reasonably.From 2018 to 2021, the total factor productivity of agricultural product cold chain logistics in a certain region is greater than 0.85, indicating that the level of total factor productivity is relatively high during this time period, and the increase in the efficiency of technical cold chain logistics is the main reason for the increase in total factor productivity.

Journal: Computational intelligence and neuroscience (2022)
Publication types: Journal Article
Correction to: Tizoxanide induces autophagy by inhibiting PI3K/Akt/mTOR pathway in RAW264.7 macrophage cells.

Unfortunately in the original publication of the article, the fig.2 was missed in the pdf version of the article which is given in this correction.The original article has been corrected.

Journal: Archives of pharmacal research (2020)
Publication types: Journal Article;Published Erratum