gebhart/patrepeval huggingface dataset:
Alpha-Fetoprotein- and CD40Ligand-Expressing Dendritic Cells for Immunotherapy of Hepatocellular Carcinoma (2021)

Dendritic cells (DC) as professional antigen presenting cells are able to prime T-cells against the tumor-associated antigen α-fetoprotein (AFP) for immunotherapy of hepatocellular carcinoma (HCC). However, a strong immunosuppressive tumor environment limits their efficacy in patients. The co-stimulation with CD40Ligand (CD40L) is critical in the maturation of DC and T-cell priming. In this study, the impact of intratumoral (i.t.) CD40L-expressing DC to improve vaccination with murine (m)AFP-transduced DC (Ad-mAFP-DC) was analyzed in subcutaneous (s.c.) and orthotopic murine HCC. Murine DC were adenovirally transduced with Ad-mAFP or Ad-CD40L. Hepa129-mAFP-cells were injected into the right flank or the liver of C3H-mice to induce subcutaneous (s.c.) and orthotopic HCC. For treatments, 10<sup>6</sup> Ad-mAFP-transduced DC were inoculated s.c. followed by 10<sup>6</sup> CD40L-expressing DC injected intratumorally (i.t.). S.c. inoculation with Ad-mAFP-transduced DC, as vaccine, induced a delay of tumor-growth of AFP-positive HCC compared to controls. When s.c.-inoculation of Ad-mAFP-DC was combined with i.t.-application of Ad-CD40L-DC synergistic antitumoral effects were observed and complete remissions and long-term survival in 62% of tumor-bearing animals were achieved. Analysis of the tumor environment at different time points revealed that s.c.-vaccination with Ad-mAFP-DC seems to stimulate tumor-specific effector cells, allowing an earlier recruitment of effector T-cells and a Th1 shift within the tumors. After i.t. co-stimulation with Ad-CD40L-DC, production of Th1-cytokines was strongly increased and accompanied by a robust tumor infiltration of mature DC, activated CD4<sup>+</sup>-, CD8<sup>+</sup>-T-cells as well as reduction of regulatory T-cells. Moreover, Ad-CD40L-DC induced tumor cell apoptosis. Intratumoral co-stimulation with CD40L-expressing DC significantly improves vaccination with Ad-mAFP-DC in pre-established HCC in vivo. Combined therapy caused an early and strong Th1-shift in the tumor environment as well as higher tumor apoptosis, leading to synergistic tumor regression of HCC. Thus, CD40L co-stimulation represents a promising tool for improving DC-based immunotherapy of HCC.
Comparison of PAM Formats for 200 Gb/s Short Reach Transmission Systems (2020)

We compared the performance of PAM4, PAM6 and PAM8 experimentally at 224/225 Gb/s using different DSP schemes including Tomlinson-Harashima precoding (THP). PAM6 shows the best overall performance. For PAM4 THP shows a large gain.
Micro/nano acoustofluidics: materials, phenomena, design, devices, and applications (2018)

Acoustic actuation of fluids at small scales may finally enable a comprehensive lab-on-a-chip revolution in microfluidics, overcoming long-standing difficulties in fluid and particle manipulation on-chip. In this comprehensive review, we examine the fundamentals of piezoelectricity, piezoelectric materials, and transducers; revisit the basics of acoustofluidics; and give the reader a detailed look at recent technological advances and current scientific discussions in the discipline. Recent achievements are placed in the context of classic reports for the actuation of fluid and particles via acoustic waves, both within sessile drops and closed channels. Other aspects of micro/nano acoustofluidics are examined: atomization, translation, mixing, jetting, and particle manipulation in the context of sessile drops and fluid mixing and pumping, particle manipulation, and formation of droplets in the context of closed channels, plus the most recent results at the nanoscale. These achievements will enable applications across the disciplines of chemistry, biology, medicine, energy, manufacturing, and we suspect a number of others yet unimagined. Basic design concepts and illustrative applications are highlighted in each section, with an emphasis on lab-on-a-chip applications.
Response to Comments on " 'Stemness': Transcriptional Profiling of Embryonic and Adult Stem Cells" and "A Stem Cell Molecular Signature" (2003)

Today, biologists can define biological processes in molecular language by acquiring global gene expression profiles. Rigorous comparison of data sets from numerous laboratories is necessary to extract biological insights. Often, this is not without complications. The comments by Fortunel et al
CEP1612, a dipeptidyl proteasome inhibitor, induces p21WAF1 and p27KIP1 expression and apoptosis and inhibits the growth of the human lung adenocarcinoma A-549 in nude mice. (2001)

The ubiquitin proteasome system is responsible for the proteolysis of important cell cycle and apoptosis-regulatory proteins. In this paper we report that the dipeptidyl proteasome inhibitor, phthalimide-(CH2)8CH-(cyclopentyl) CO-Arg(NO2)-Leu-H (CEP1612), induces apoptosis and inhibits tumor growth of the human lung cancer cell line A-549 in an in vivo model. In cultured A-549 cells, CEP1612 treatment results in accumulation of two proteasome natural substrates, the cyclin-dependent kinase inhibitors p21WAF1 and p27KIP1, indicating its ability to inhibit proteasome activity in intact cells. Furthermore, CEP1612 induces apoptosis as evident by caspase-3 activation and poly(ADP-ribose) polymerase cleavage. Treatment of A-549 tumor-bearing nude mice with CEP1612 (10 mg/kg/day, i.p. for 31 days) resulted in massive induction of apoptosis and significant (68%; P < 0.05) tumor growth inhibition, as shown by terminal deoxynucleotidyltransferase-mediated UTP end labeling. Furthermore, immunostaining of tumor specimens demonstrated in vivo accumulation of p21WAF1 and p27KIP1 after CEP1612 treatment. The results suggest that CEP1612 is a promising candidate for further development as an anticancer drug and demonstrate the feasibility of using proteasome inhibitors as novel antitumor agents.
Table S5. DAVID functional classification of ixazomib genes. from Proteasomal Inhibition by Ixazomib Induces CHK1 and MYC-Dependent Cell Death in T-cell and Hodgkin Lymphoma (2023)

&lt;p&gt;Functional annotation clusters determined from the common genes in ixazomib 25nM/24 hours vs. Control for Jurkat, L540, and L428 cells (Fig. 1C). This was determined through DAVID Gene Functional Classification Tool. The enrichment scores were determined by DAVID through the geometric mean of the EASE scores (modified Fisher Exact).&lt;/p&gt;
Structure Activity Relationship at 5-HT1A receptors within a novel series of spiro-1,3-Dioxolane-based ligands (2006)

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Supplementary Tables 1-2 from Fc Optimization of Therapeutic Antibodies Enhances Their Ability to Kill Tumor Cells <i>In vitro</i> and Controls Tumor Expansion <i>In vivo</i> via Low-Affinity Activating Fcγ Receptors (2023)

Supplementary Tables 1-2 from Fc Optimization of Therapeutic Antibodies Enhances Their Ability to Kill Tumor Cells &lt;i&gt;In vitro&lt;/i&gt; and Controls Tumor Expansion &lt;i&gt;In vivo&lt;/i&gt; via Low-Affinity Activating Fcγ Receptors
From Cookies to Cooks: Insights on Dietary Patterns via Analysis of Web Usage Logs (2013)

Nutrition is a key factor in people's overall health. Hence, understanding the nature and dynamics of population-wide dietary preferences over time and space can be valuable in public health. To date, studies have leveraged small samples of participants via food intake logs or treatment data. We propose a complementary source of population data on nutrition obtained via Web logs. Our main contribution is a spatiotemporal analysis of population-wide dietary preferences through the lens of logs gathered by a widely distributed Web-browser add-on, using the access volume of recipes that users seek via search as a proxy for actual food consumption. We discover that variation in dietary preferences as expressed via recipe access has two main periodic components, one yearly and the other weekly, and that there exist characteristic regional differences in terms of diet within the United States. In a second study, we identify users who show evidence of having made an acute decision to lose weight. We characterize the shifts in interests that they express in their search queries and focus on changes in their recipe queries in particular. Last, we correlate nutritional time series obtained from recipe queries with time-aligned data on hospital admissions, aimed at understanding how behavioral data captured in Web logs might be harnessed to identify potential relationships between diet and acute health problems. In this preliminary study, we focus on patterns of sodium identified in recipes over time and patterns of admission for congestive heart failure, a chronic illness that can be exacerbated by increases in sodium intake.
Automatic Labeling for Scene Text Database (2013)

It is thought that a large quantity of data improve quality of recognition. A large database, however, is not easy to obtain. The hardest task is labeling (also known as ground truthing), which usually requires human intervention. Since labeling by human is laborious and costly, labeling without human (automatic labeling) or minimization of human intervention (semi-automatic labeling) are ideal scenarios. As a step toward realization of the scenarios, knowing how much an automatic labeling system can perform without human intervention is important. In the current paper we propose a comprehensive automatic labeling technique for a scene text database, which performs segmentation and labeling for unsegmented and unlabeled character images. To our best knowledge, this is the first method to realize the comprehensive process for automatic labeling for scene text databases In experiments, we confirmed that the proposed method could add new unlabeled data in parallel with improving recognition performance of the classifier.
Adenosine triphosphate–dependent calcium signaling during ventilator-induced lung injury is amplified by hypercapnia (2011)

Adenosine triphosphate (ATP) is released by alveolar epithelial cells during ventilator-induced lung injury (VILI) and regulates fluid transport across epithelia. High CO(2) levels are observed in patients with "permissive hypercapnia," which inhibits alveolar fluid reabsorption (AFR) in alveolar epithelial cells. The authors set out to determine whether VILI affects AFR and whether the purinergic pathway is modulated in cells exposed to hypercapnia. Control group was compared against VILI (tidal volume [Vt] = 35 mL/kg, zero positive end-expiratory pressure [PEEP]) and protective ventilation (Vt = 6 mL/kg, PEEP = 10 cm H(2)O) groups. Lung mechanics, histology, and AFR were evaluated. Alveolar epithelial cells (AECs) were loaded with Fura 2-AM to measure intracellular calcium in the presence ATP (10 μM) at 5% or 10% CO(2) as compared with baseline. High tidal volume ventilation impairs lung mechanics and AFR. Hypercapnia (HC) increases intracellular calcium levels in response to ATP stimulation. HC + ATP is the most detrimental combination decreasing AFR. Purinergic signaling in AECs is modulated by high CO(2) levels via increased cytosolic calcium. The authors reason that this modulation may play a role in the impairment of alveolar epithelial functions induced by hypercapnia.
Pore-size Controlled and Polycation-immobilized Cellulose Spherical Particles for Removal of Endotoxin (2007)

セルロース微粒子を基材とし，これに種々のポリカチオンを化学修飾した高分子球状微粒子を調製した．得られた種々のポリカチオン固定化セルロース粒子をエンドトキシン(LPS)吸着剤として用い，バッチ法により LPS 水溶液からの LPS 吸着除去を試みた．その結果，すべての粒子の LPS 吸着能は，粒子の細孔径(糖の排除限界分子；Mlim)の増大とともに著しく増大し，吸着時の緩衝液のイオン強度の上昇とともに低下した．種々の吸着剤のタンパク質溶液からの LPS 選択除去能をカラム法により評価した結果，ポリ(ε-リジン)固定化セルロース粒子は pH 7，イオン強度 μ=0.17 の条件下で，アルブミンを吸着することなく，LPS を吸着除去できた．吸着処理後の溶液中の LPS 残存濃度は 10 pg/mL 以下で，タンパク質回収率は 98%であった．これらの結果から，同粒子はタンパク質水溶液からの LPS 吸着除去剤として大いに期待できることがわかった．
Sertoli Cells Induce Systemic Donor-Specific Tolerance in Xenogenic Transplantation Model (2006)

Cell therapy is a potentially powerful tool in the treatment of many grave disorders including leukemia, immune deficiencies, autoimmune diseases, and diabetes. However, finding matched donors is challenging and recipients may suffer from the severe complications of systemic immune suppression. Sertoli cells, when cotransplanted with both allo- and xenograft tissues, promote graft acceptance in the absence of systemic immunosuppression. How Sertoli cells do this is not, as yet, clearly defined. We have examined the ability of Sertoli cells to produce systemic immune tolerance. For this purpose, Sertoli cells were injected into an otherwise normal C57/BL6 mouse host via the lateral tail vein. No other immunosuppressive protocols were applied. Six to 8 weeks posttransplantation, blood was collected for analysis of cytokine levels. Tolerance to donor cells was determined by mixed lymphocytic culture, and production of T-cell-dependent antibody was determined by an in vitro anti-sheep red blood cell plaque-forming assay. Results showed a marked modulation of immune cytokines in the transplanted mouse host and donor-specific transplantation tolerance was achieved. Tolerant mouse lymphocytes maintained a competent humoral antibody response. Additionally, C57/BL6 mice transplanted with rat Sertoli cells tolerated rat skin grafts significantly longer than control non-Sertoli cell transplanted mice. We conclude that systemic administration of rat Sertoli cells across xenogenic barrier induces transplantation tolerance without altering systemic immune competence. These data suggest that Sertoli cells may be used as a novel and potentially powerful tool in cell transplantation therapy.
Ultrasound Radiation as a “Throwing Stones” Technique for the Production of Antibacterial Nanocomposite Textiles (2010)

Ultrasound irradiation was applied as a "throwing stones" technique for coating cotton bandages with MgO and Al(2)O(3) commercially obtained nanoparticles. The homogeneous distribution of the nanoparticles without any aggregation on the fabrics was demonstrated. The antibacterial activities of the MgO/Al(2)O(3)-fabric nanocomposite were tested against Escherichia coli (Gram negative) and Staphylococcus aureus (Gram positive) cultures. A significant bactericidal effect, even in a concentration <1% (by weight), was detected.
High Prevalence of &lt;i&gt;Enterobius vermicularis&lt;/i&gt; Infection among Schoolchildren in Three Townships around Yangon, Myanmar (2015)

In order to determine the status of Enterobius vermicularis infection among schoolchildren in suburban areas of Myanmar, 761 primary schoolchildren in 3 different townships around Yangon City were subjected to a survey using cello-tape anal swabs. The subjected schoolchildren were 383 boys and 378 girls who were 5-7 years of age. Only 1 anal swab was obtained from each child. The overall egg positive rate of E. vermicularis was 47.2% (359 positives), and sex difference was not remarkable (48.6% in boys and 45.8% in girls). However, the positive rate was the highest in South Dagon (54.6%) followed by Hlaing Thayar (43.8%) and North Dagon (34.8%). This difference was highly correlated with the living standards of the people in each township. Nucleotide sequence of the 5S rDNA from the eggs on the cello-tape (2 children) revealed 99.7% identity with that of E. vermicularis reported in GenBank. The results indicated that E. vermicularis infection is highly prevalent among primary schoolchildren around Yangon, Myanmar.
Development and validation of a residual risk score to predict breast cancer risk in unaffected women negative for mutations on a multi-gene hereditary cancer panel. (2017)

1579 Background: Women who are unaffected with cancer but have a significant family history of breast cancer (BC) are frequently referred for hereditary cancer testing with multi-gene panels; however, &lt; 10% test positive for clinically actionable mutations. Large-scale genotyping studies have identified common variants (primarily single-nucleotide polymorphisms) that individually confer modest BC risk, but together may explain the genetic susceptibility for BC in many women without monogenic mutations. Here, we describe the development and validation of a polygenic residual risk score in a large, consecutive cohort of women who tested negative for mutations in known BC susceptibility genes. Methods: This IRB-approved study includes women of European ancestry tested with a multi-gene hereditary cancer panel who were negative for mutations in 11 genes associated with BC ( BRCA1, BRCA2, TP53, PTEN, STK11, CDH1, PALB2, CHEK2, ATM, NBN, BARD1). Clinical information was collected from provider-completed test request forms. The dataset was divided into a training (July – November 2016) and validation cohort (November 2016 – April 2017). Multivariable logistic regression models were used to evaluate 94 common variants and develop candidate residual risk scores as predictors of personal BC history (invasive ductal carcinoma, IDC) in the training cohort. Independent variables included age, personal/family cancer history, and ancestry. An optimal subset of the 94 common variants and a residual risk score will be selected through cross-validation followed by independent validation. Results: The training cohort includes 11,838 women (median age 47 years), 18% of whom reported a personal history of IDC and 36% of whom reported BC in a first-degree relative. Results from validation of the residual risk score in an independent cohort of approximately 12,000 women will be completed at the time of presentation. Conclusions: The validation and clinical implementation of a residual risk score for women at risk for hereditary BC may offer significant potential for the management of high-risk, unaffected women who test negative for monogenic BC mutations.
Third generation disease models: Image analysis tools, pediatric heart diseases, inflammatory diseases and brain tumors (2010)

Welcome to the Health-e-Child deliverable D11.4. Following the web-based format initiated for previous deliverables of WP11, this public deliverable is giving the last update on the state of our disease models from a high level point of view. These web-pages update and replace the ones of deliverable D11.3. The document is organised in 5 parts: the first three parts corresponding to the current status of each task of the work-package, organised by disease. Then, two part describe the more generic image registration and shape analysis tools developped in the project.
Coevolution of Security’s Body of Knowledge and Curricula (2021)

Reviews efforts to capture the body of knowledge in cybersecurity or computer and Internet security (CIS) more specifically and discuss related curricular frameworks. The aim is to increase awareness of resources to guide topic selection of CIS courses for educational and training programs.
Communication security for smart grid distribution networks (2013)

The operation and control of the next generation electrical grids will depend on a complex network of computers, software, and communication technologies. Being compromised by a malicious adversary would cause significant damage, including extended power outages and destruction of electrical equipment. Moreover, the implementation of the smart grid will include the deployment of many new enabling technologies such as advanced sensors and metering, and the integration of distributed generation resources. Such technologies and various others will require the addition and utilization of multiple communication mechanisms and infrastructures that may suffer from serious cyber vulnerabilities. These need to be addressed in order to increase the security and thus the greatest adoption and success of the smart grid. In this article, we focus on the communication security aspect, which deals with the distribution component of the smart grid. Consequently, we target the network security of the advanced metering infrastructure coupled with the data communication toward the transmission infrastructure. We discuss the security and feasibility aspects of possible communication mechanisms that could be adopted on that subpart of the grid. By accomplishing this, the correlated vulnerabilities in these systems could be remediated, and associated risks may be mitigated for the purpose of enhancing the cyber security of the future electric grid.
Exterior moment method analysis of conducting scatterers by using the interior Green's function and the method of least square (1992)

A method previously proposed by the authors in 1988 for obtaining the mutual admittance matrix in the moment method analysis by using the interior Green's function is improved by introducing the method of least square (MLS). A numerical example of a two-dimensional problem shows that accurate results can be obtained by introducing the MLS even when arbitrary sources are assumed for numerical experiments in the interior region.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
FOXA2 suppresses endometrial carcinogenesis and epithelial-mesenchymal transition by regulating enhancer activity (2022)

FOXA2 encodes a transcription factor mutated in 10% of endometrial cancers (ECs), with a higher mutation rate in aggressive variants. FOXA2 has essential roles in embryonic and uterine development. However, FOXA2's role in EC is incompletely understood. Functional investigations using human and mouse EC cell lines revealed that FOXA2 controls endometrial epithelial gene expression programs regulating cell proliferation, adhesion, and endometrial-epithelial transition. In live animals, conditional inactivation of Foxa2 or Pten alone in endometrial epithelium did not result in ECs, but simultaneous inactivation of both genes resulted in lethal ECs with complete penetrance, establishing potent synergism between Foxa2 and PI3K signaling. Studies in tumor-derived cell lines and organoids highlighted additional invasion and cell growth phenotypes associated with malignant transformation and identified key mediators, including Myc and Cdh1. Transcriptome and cistrome analyses revealed that FOXA2 broadly controls gene expression programs through modification of enhancer activity in addition to regulating specific target genes, rationalizing its tumor suppressor functions. By integrating results from our cell lines, organoids, animal models, and patient data, our findings demonstrated that FOXA2 is an endometrial tumor suppressor associated with aggressive disease and with shared commonalities among its roles in endometrial function and carcinogenesis.
Experiments with Large-Mirror-Ratio Corrugation at Multiple Mirror Trap GOL-3 (2009)

New operation regime with a high-mirror-ratio corrugation at first 2 meters of GOL-3 plasma was studied. Five corrugation periods of 44 cm length were created with mirror ratio R ≈ 2.7 by means of special configuration of a power feed of existing solenoid coils. First data on the plasma heating, confinement and features of neutron emission from the strongly corrugated plasma in the above conditions are presented.