gebhart/patrepeval huggingface dataset:
Impact of in vitro chemosensitivity test-guided platinum-based adjuvant chemotherapy on the surgical outcomes of patients with p-stage IIIA non-small cell lung cancer that underwent complete resection (2017)

The impact of <i>in vitro</i> chemosensitivity test-guided platinum-based adjuvant chemotherapy on the surgical outcomes of patients undergoing complete resection for locally advanced non-small cell lung cancer (NSCLC) has yet to be elucidated. In the present study, the utility of adjuvant chemotherapy based on the collagen gel droplet embedded culture drug sensitivity test (CD-DST) in patients with p (pathology)-stage IIIA NSCLC was retrospectively analyzed. A series of 39 patients that had received platinum-based adjuvant chemotherapy following complete resection between 2007 and 2012 were enrolled. Their surgical specimens were subjected to the CD-DST. The patients were subsequently classified into two groups on the basis of <i>in vitro</i> anti-cancer drug sensitivity data obtained using the CD-DST: The sensitive group (25 patients) were treated with regimens including one or two of the anti-cancer drug(s) that were indicated to be effective by the CD-DST, whereas the non-sensitive group (14 patients) were treated with chemotherapy regimens that did not include any CD-DST-selected anti-cancer drugs. There were no significant differences in the background characteristics of the two groups [including in respect of the pathological TN (tumor-lymph node) stage, tumor histology, epidermal growth factor receptor mutation status, the frequency of each chemotherapy regimen, and the number of administered cycles]. The 5-year disease-free survival (DFS) rate of the sensitive group was 32.3%, whereas that of the non-sensitive group was 14.3% (P=0.037). In contrast, no difference in overall survival (OS) was observed (P=0.76). Multivariate analysis revealed that adjuvant chemotherapy based on the CD-DST had a significant favorable effect on the DFS (P=0.01). Therefore, the present study has demonstrated that CD-DST data obtained from surgical specimens aid the selection of effective platinum-based adjuvant chemotherapy regimens for patients undergoing complete resection for p-stage IIIA NSCLC. The use of CD-DST-guided platinum-based regimens may have a beneficial impact on the DFS of such patients.
Gender HCI (2010)

Although there has been recent investigation into how to understand and ameliorate the low representation of females in computing, there has been little research into how software itself fits into the picture. Our focus is on how supposedly gender-neutral software interacts with gender differences. Specifically, we have concentrated on software aimed at supporting users doing problem solving. For example, what if females' problem-solving effectiveness, using software such as Excel, would accelerate if the software were changed to take gender differences into account? This talk reports the investigations my students and I have conducted into whether and how software and its features affect females' and males' performance differently, and describes the beginnings of work on promising interventions that help both males and females.
Monoclonal anti-acetylcholine receptor antibodies with differing capacities to induce experimental autoimmune myasthenia gravis. (1985)

To study the characteristics of the individual autoantibodies that are important in the development of an autoimmune disease, we produced 26 anti-acetylcholine receptor (anti-AChR) monoclonal antibodies (mcAb) and studied the experimental autoimmune myasthenia gravis (EAMG) induced by a number of them. The mcAb reactive with mammalian acetylcholine receptor (M-AChR) exhibited a wide range of dissociation rates from in situ M-AChR of motor endplates. All anti-M-AChR mcAb were capable of producing at least some degree of histopathologic change at the endplate indicative of EAMG, but their potencies varied markedly. One mcAb induced, even at large doses, only minor macrophage invasion without clinical or electromyographic effect. Others induced severe EAMG, and even death, at 1/200th the dose. Low potency was associated with high rate of mcAb dissociation from antigen. High potency was associated with intermediate avidity, not high avidity. These observations suggest that in EAMG, and perhaps in myasthenia gravis, the characteristics of the individual antibodies making up the autoimmune response can determine the severity of the autoimmune disease.
Video 1 - ATMi increases the rate of mitotic catastrophe in glioma cells when p53 is knocked down. from Orally Bioavailable and Blood–Brain Barrier-Penetrating ATM Inhibitor (AZ32) Radiosensitizes Intracranial Gliomas in Mice (2023)

&lt;p&gt;U87/Centrin2-EGFP/H2B-mCherry/puro cells were seeded on dishes with cover slip bottoms and irradiated (5 Gy). Time-lapse videos were recorded intermittently (every 7 min) over 16 hrs. Treatment results in 2.7% aberrant mitoses (see Fig. 3F).&lt;/p&gt;
Cytokine Induction byStreptococcus mutansand Pulpal Pathogenesis (2000)

Chronic pulpal inflammation under caries appears to be elicited by bacterial antigens that diffuse into the pulp through dentinal tubules. This prompted the hypothesis that cytokines elicited by antigens from Streptococcus mutans, which frequently dominates shallow lesions, could play a major role in eliciting the initial T-cell response in the pulp. To test this, we examined the ability of S. mutans to stimulate T cells and elicit cytokines and used Lactobacillus casei, which often predominates in deep carious lesions where B cells and plasma cells predominate, as a control. In addition, the presence of cytokines in the pulp was analyzed at the mRNA level. S. mutans elicited potent gamma interferon (IFN-gamma) responses in peripheral blood mononuclear cell cultures and reduced the CD4/CD8 ratio by promoting CD8(+) T cells. Multiple inflammatory cytokine mRNAs (IFN-gamma, interleukin 4 [IL-4], and IL-10) were detected in human dental pulp. A higher prevalence of IFN-gamma (67%) than IL-4 (19%) or IL-10 (29%) was obtained in shallow caries, suggesting a type 1 cytokine mechanism in early pulpitis where S. mutans predominates. In contrast, in deep caries no differences in cytokine frequency were observed. Furthermore, the presence of IFN-gamma in the pulp correlated with the presence of S. mutans. The extraordinary induction of type 1 cytokines and the preferential activation of CD8(+) T cells by S. mutans offers an explanation for the etiology of the CD8(+) T-cell-dominant lesion in early pulpitis and suggests that S. mutans may have a major impact on the initial lesion and pulpal pathology.
Inhibition of Tumor Cell Invasion by Ubenimex (Bestatin) in vitro (1989)

We have investigated the effect of the immunomodulator ubenimex (bestatin) on tumor cell invasion of reconstituted basement membrane (Matrigel). The invasion of B16-BL6 melanoma cells and Lewis lung carcinoma (3LL) cells into Matrigel-coated filters was inhibited by the presence of bestatin in a concentration-dependent manner. The pretreatment of either tumor cells or Matrigel with bestatin, however, had little effect on the invasion of tumor cells. Since bestatin was found to inhibit amino-peptidase in addition to its immunomodulating activities, the inhibition of tumor invasion by bestatin is likely to be associated with the action as an enzyme inhibitor. Other aminopeptidase inhibitors, arphamenine B and amastatin A, could also inhibit tumor cell invasion into Matrigel. Bestatin inhibited hydrolyzing activities towards substrates of aminopeptidases in B16-BL6 melanoma cells. However, bestatin did not have any effect on the haptotactic migration and adhesion of tumor cells to the substrates. These results indicated that bestatin may inhibit tumor cell invasion through a mechanism involving its inhibitory action on aminopeptidases in tumor cells.
Supplementary Table 4 from Endobronchial miRNAs as Biomarkers in Lung Cancer Chemoprevention (2023)

&lt;p&gt;PDF file - 73K, Association of miRNA expression at BL with response. Legend: This table reports the three miRNAs (miR-34c, miR-224, miR-375) that are significantly differentially expressed at BL in responders as compared to non-responders in at least one comparison The table shows up- or down-regulation in responders compared to non-responders. The significant p-values from Welch's t-test are reported. "FDR" indicates that the p-value is significant after adjustment for False Discovery Rate (FDR). Odds ratios (OR) were calculated by logistic regression model and reported with their 95% confidence interval and p-value. When either the t-test or the OR was significant, both are reported.&lt;/p&gt;
Androgynous Porphyrins. Silver(II) Quinoxalinoporphyrins Act as Both Good Electron Donors and Acceptors (2008)

The metal-centered and macrocycle-centered electron-transfer oxidations and reductions of silver(II) porphyrins were characterized in nonaqueous media by electrochemistry, UV-vis spectroelectrochemistry, EPR spectroscopy, and DFT calculations. The investigated compounds are {5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)porphyrinato}silver(II), {5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)quinoxalino[2,3-b']porphyrinato}silver(II), {5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)bisquinoxalino[2,3-b':7,8-b'']porphyrinato}silver(II), and {5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)bisquinoxalino[2,3-b':12,13-b'']porphyrinato}silver(II). The first one-electron oxidation and first one-electron reduction both occur at the metal center to produce stable compounds with Ag(III) or Ag(I) metal oxidation states, irrespective of the type of porphyrin ligand. The electrochemical HOMO-LUMO gap, determined by the difference in the first oxidation and first reduction potentials, decreases by introduction of quinoxaline groups fused to the Ag(II) porphyrin macrocycle. This provides a unique androgynous character to Ag(II) quinoxalinoporphyrins that enables them to act as both good electron donors and good electron acceptors, something not previously observed in other metalloporphyrin complexes. The second one-electron oxidation and second one-electron reduction of the compounds both occur at the porphyrin macrocycle to produce Ag(III) porphyrin pi-radical cations and Ag(I) porphyrin pi-radical anions, respectively. The macrocycle-centered oxidation potentials of each quinoxalinoporphyrin are shifted in a negative direction, while the macrocycle-centered reduction potentials are shifted in a positive direction as compared to the same electrode reactions of the porphyrin without the fused quinoxaline ring(s). Both potential shifts are due to a stabilization of the radical cations and radical anions by pi-extension of the porphyrin macrocycle after fusion of one or two quinoxaline moieties at the beta-pyrrolic positions of the macrocycle. Introduction of quinoxaline groups fused to the Ag(II) porphyrin macrocycle provides a unique androgynous character to Ag(II) quinoxalinoporphyrins that enables them to act as both good electron donors and good electron acceptors.
Microfabricated packed‐bed reactor for phosgene synthesis (2001)

Abstract A silicon micropacked‐bed reactor for phosgene synthesis is demonstrated as an example of the potential for safe on‐site/on‐demand production of a hazardous compound. Complete conversion of chlorine is observed for both a 2:1 CO/Cl 2 feed at 4.5 std. cm 3 /min and a 1:1 feed at 8 std. cm 3 /min. The latter gives a projected productivity of ∼100 kg/yr from a 10‐channel microreactor, with the opportunity to produce significant quantities through operating many reactors in parallel. The versatility of silicon microfabrication technology for producing reactors for corrosive gases is demonstrated by a protective oxide coating formed during reactor fabrication. The increased heat and mass transfer inherent at the submillimeter reactor length scale provides a larger degree of safety, control, and suppression of gradients than is available in macroscale systems. These advantages are also explored in the extraction of chemical kinetics from microreactor experiments. The preexponential factor and apparent activation energy for phosgene formation are determined demonstrating the utility of micropacked‐bed reactors as laboratory research tools.
Immunogenicity and protective efficacy of a recombinant filamentous haemagglutinin from Bordetella pertussis (2006)

Bordetella pertussis is the causative agent of whooping cough, a major childhood pathogen; acellular vaccines consisting of purified B. pertussis antigens such as filamentous haemagglutinin (FHA) are commonly used to prevent pertussis. Despite the importance of FHA in B. pertussis pathogenesis and its inclusion in most acellular vaccines, the functional importance of individual domains in the induction of protective immunity is largely unknown. In this study, we have purified a recombinant FHA protein from Escherichia coli consisting of a 42 kDa maltose binding domain of E. coli and the 43 kDa type I immunodominant domain of FHA. The fusion protein (Mal85) was purified from E. coli cell lysates via affinity chromatography with an amylose column. Mal85 was then delivered to BALB/c mice intranasally encapsulated in liposomes, formulated with Protollin(TM) or in conjunction with an immunostimulatory CpG oligonucleotide. Mice were also vaccinated intraperitoneally with alum-adsorbed Mal85. Sera from all treatment groups showed strong IgG responses to Mal85 and recognized native FHA. Specific salivary IgA was induced in mice vaccinated with Mal85 in liposomes, Protollin(TM) and delivered with CpG. Vaccination with Mal85 encapsulated in liposomes or formulated with Protollin(TM) provided protection against aerosol challenge with B. pertussis in BALB/c mice. These data indicate that the type I domain of FHA is a protective antigen in mice and may serve as a candidate for inclusion in new acellular pertussis vaccines.
Surprise: Result List Truncation via Extreme Value Theory (2023)

Work in information retrieval has largely been centered around ranking and relevance: given a query, return some number of results ordered by relevance to the user. The problem of result list truncation, or where to truncate the ranked list of results, however, has received less attention despite being crucial in a variety of applications. Such truncation is a balancing act between the overall relevance, or usefulness of the results, with the user cost of processing more results. Result list truncation can be challenging because relevance scores are often not well-calibrated. This is particularly true in large-scale IR systems where documents and queries are embedded in the same metric space and a query's nearest document neighbors are returned during inference. Here, relevance is inversely proportional to the distance between the query and candidate document, but what distance constitutes relevance varies from query to query and changes dynamically as more documents are added to the index. In this work, we propose Surprise scoring, a statistical method that leverages the Generalized Pareto Distribution that arises in extreme value theory to produce interpretable and calibrated relevance scores at query time using nothing more than the ranked scores. We demonstrate its effectiveness on the result list truncation task across image, text, and IR datasets and compare it to both classical and recent baselines. We draw connections to hypothesis testing and p-values.
Melatonin enhances vertical bone augmentation in rat calvaria secluded spaces (2015)

Melatonin promoted vertical bone regeneration in rat calvaria in the secluded space within the plastic cap.
Aqueous extract of freeze-dried Protaetia brevitarsis larvae promotes osteogenesis by activating β-catenin signaling (2022)

Objective: To investigate the effect of an aqueous extract of Protaetia brevitarsis (AEPB) on osteogenesis using preosteoblast MC3T3-E1 cells and zebrafish larvae. Methods: Flow cytometric analysis was used to measure the cytotoxicy. Alkaline phosphatase activity was detetmined using p-nitrophenyl phosphate as a substrate. Calcium deposition was detected using alizarin red staining along with osteogenic marker expression in preosteoblast MC3T3E1 cells. In addition, vertebral formation in zebrafish larvae was detected using calcein staining and osteogenic gene expression. Results: AEPB highly promoted the expression of osteogenic markers including runt-related transcription factor 2, osterix, and alkaline phosphatase, along with elevated levels of mineralization in MC3T3-E1 cells. Moreover, AEPB accelerated vertebral formation in zebrafish larvae accompanied by upregulated expression of osteogenic genes. FH535, an inhibitor of Wnt/β-catenin, suppressed AEPB-induced osteogenic gene expression and vertebral formation, indicating that AEPB stimulates osteogenesis by activating the Wnt/β-catenin signaling pathway. Conclusions: AEPB stimulates osteoblast differentiation and bone formation by activating β-catenin. Therefore, AEPB is a promising material that induces osteogenesis, and is useful for the treatment of bone resorption diseases.
Association Between Wilms Tumor and Gonadal Dysgenesis (1981)

The classification of intersexuality was determined in 10 patients with an intersex disorder who subsequently suffered a Wilms tumor. Of these 10 patients 7 (70 per cent) had a disorder of gonadal dysgenesis: 5 had mixed gonadal dysgenesis, 1 had dysgenetic male pseudohermaphroditism and 1 had 46XY pure gonadal dysgenesis. Because the gonads of patients with either of these 3 disorders have a high predilection for the development of testicular neoplasia, the concomitant occurrence of renal tumors in such a patient population suggests that a common defect in the urogenital ridge, the embryonic precursor of the kidneys and gonads, may be the cause of this association.
Inhibition of NF-kappa B activity in human T lymphocytes induces caspase-dependent apoptosis without detectable activation of caspase-1 and -3. (1999)

NF-kappa B is involved in the transcriptional control of various genes that act as extrinsic and intrinsic survival factors for T cells. Our findings show that suppression of NF-kappa B activity with cell-permeable SN50 peptide, which masks the nuclear localization sequence of NF-kappa B1 dimers and prevents their nuclear localization, induces apoptosis in resting normal human PBL. Inhibition of NF-kappa B resulted in the externalization of phosphatidylserine, induction of DNA breaks, and morphological changes consistent with apoptosis. DNA fragmentation was efficiently blocked by the caspase inhibitor Z-VAD-fmk and partially blocked by Ac-DEVD-fmk, suggesting that SN50-mediated apoptosis is caspase-dependent. Interestingly, apoptosis induced by NF-kappa B suppression, in contrast to that induced by TPEN (N,N,N',N'-tetrakis [2-pyridylmethyl]ethylenediamine) or soluble Fas ligand (CD95), was observed in the absence of active death effector proteases caspase-1-like (IL-1 converting enzyme), caspase-3-like (CPP32/Yama/apopain), and caspase-6-like and without cleavage of caspase-3 substrates poly(ADP-ribose) polymerase and DNA fragmentation factor-45. These findings suggest either low level of activation is required or that different caspases are involved. Preactivation of T cells resulting in NF-kappa B nuclear translocation protected cells from SN50-induced apoptosis. Our findings demonstrate an essential role of NF-kappa B in survival of naive PBL.
Micromagnetism and magnetization reversal of micron-scale (110) Fe thin-film magnetic elements (1999)

Magnetic force microscope (MFM) imaging in conjunction with longitudinal Kerr hysteresis loop measurements have been used to investigate the micromagnetic behavior of micron scale epitaxial (110) bcc Fe thin-film elements (50-nm thick) with rectangular, triangular, and needle-shaped ends and competing magnetic anisotropies. Thin-film elements of $2\ensuremath{-}\ensuremath{\mu}\mathrm{m}$ width and $6\ensuremath{-}\ensuremath{\mu}\mathrm{m}$ length and greater have been fabricated with their long axis oriented either parallel or perpendicular to the [001] in-plane magnetocrystalline easy axis. For elements with their long axis perpendicular to the [001] direction, the end shape is critical in determining domain nucleation, domain configurations, and magnetic hysteresis. The magnetization reversal mechanisms are revealed by direct field dependent MFM imaging. Magnetic vortex configurations within elements during reversal are seen to be affected by small changes in element corner shape. Similarly, small trapped domains and domain walls are observed to applied fields significantly larger than the coercive field and apparent magnetic saturation field, as determined by hysteresis loop measurements of arrays of elements. These are shown to have a dramatic effect on the character of the low-field magnetic hysteresis. Particles with long axis parallel to the [001] direction have large remanence and switching fields which also depend sensitively on end shape. The angular dependence of the switching field observed in these elements is contrasted to that of magnetization reversal by coherent rotation.
Numerical verification of degeneracy in hexagonal photonic crystal fibers (2001)

Modal birefringences in photonic crystal fibers with six air holes symmetrically arranged around the core region and with multiple air holes in a hexagonal lattice are numerically investigated in detail. It is confirmed from the computed results obtained by a full-vector finite element method that both the hexagonal holey fibers are not birefringent, namely, the two fundamental modes are degenerate.
Heterogeneous Integration Using Organic Interposer Technology (2020)

As the costs of advanced node silicon have risen sharply with the 7 and 5-nanometer nodes, advanced packaging is coming to a crossroad where it is no longer fiscally prudent to pack all desired functionality into a single die. While single-die packages will still be around, the high-end market is shifting towards multiple-die packages to reduce overall costs and improve functionality. This shift is not just to add local memory, such as the addition of high-bandwidth memory (HBM) module(s) to an application-specific integrated circuit (ASIC) die, but also to separate what would have been a monolithic ASIC in prior generations to its constituent parts, such as the central processing unit (CPU) cores, serializer/deserializer (SerDes) and input/output (I/O) blocks. By splitting the monolithic die into smaller functional blocks, costs can be reduced through improved wafer yield on the smaller CPU cores and re-using older, vetted intellectual property (IP) from a prior silicon node for the I/O and SerDes that do not necessarily need the most advanced silicon node.The traditional approach to fine-pitch multi-die packaging has been silicon interposers with Through Silicon Vias (TSVs). While the TSV approach has ushered in new performance levels never seen before, one of the major limitations is the inability to scale with higher and higher frequencies. The maximum frequency that a silicon interposer can handle between die-to-die interconnects is approximately 4 GHz due to the parasitics of the silicon. As dieto-die interconnects increase their bandwidth to higher and higher levels, the 4-6 GHz limitation can become a major bottleneck. Eliminating the silicon and silicon dioxide dielectrics and using polymers as the dielectric and the interposer itself can solve this problem.This paper will discuss how to use High-Density Fan-Out (HDFO) technology to replace the TSV-bearing silicon interposer with an organic interposer to enable higher bandwidth die-to-die interconnects for heterogeneous integration.