gebhart/patrepeval huggingface dataset:
Structural Insight into Guest Binding Sites in a Porous Homochiral Metal–Organic Material (2015)

An enantiomeric pair of chiral metal-organic materials (CMOMs) based upon mandelate (man) and 4,4'-bipyridine (bpy) ligands, [Co2(S-man)2(bpy)3](NO3)2·guest (1S·guest) and [Co2(R-man)2(bpy)3](NO3)2·guest (1R·guest), have been prepared. The cationic frameworks exhibit one-dimensional chiral channels with dimensions of 8.0 Å × 8.0 Å. The pore chemistry is such that chiral surfaces lined with nitrate anions and phenyl groups create multiple binding sites for guest and/or solvent molecules. The performance of 1S and 1R with respect to resolution of racemic mixtures of 1-phenyl-1-propanol (PP) was studied by varying time, temperature, and the use of additives. Selectivity toward PP was determined by chiral HPLC with ee values of up to 60%. The binding sites and host-guest interactions were investigated through single-crystal X-ray structural analyses of guest-exchanged 1S and 1R. Crystallographically observed structural changes (e.g., the absolute configurations of the three PP binding sites switch from R, R, and S to R, R, and R/S) correlate with experimentally observed ee values of 33% and 60% for variants of 1S that contain PP and different solvent molecules, 1S·PPex and 1S·PPex', respectively. The fact that manipulation of guest solvent molecules, which in effect serve as cofactors, can modify chiral sites and increase enantioselectivity is likely to aid in the design of more effective CMOMs and processes for chiral separations.
Pulpal Responses to Various Dentin Bonding Systems in Dentin Cavities (1991)

The purpose of this study was to investigate pulpal response and bacterial invasion associated with five dentin bonding systems placed in cavities without an enamel margin. Two hundred and twenty-four dentin margin cavities were created by removing the surrounding marginal enamel of class V cavities in monkey teeth. These cavities were restored with a resin composite using various current dentin bonding systems. All of the dentin bonding systems showed odontoblastic layer changes to varying degrees, and slight to moderate inflammation at the initial stage. With the lapse of time, the degree of inflammation tended to decrease markedly, except for those cases in which bacteria were present. The result of SA/Photo Bond corresponded to that of the glass ionomer cement (negative control). Accordingly, this study suggests that a good bond and adaptation between resin and dentin should be obtained for eliminating pulpal irritation, even in the dentin cavity.
Cartilage viability after trochleoplasty (2006)

Trochleoplasty is an established and accepted technique for the treatment of patellar instability because of a missing trochlear groove. In this technique, a flap of cartilage over the trochlea is carefully removed and a new trochlear groove is created in the underlying bone before the cartilaginous flap is reattached with sutures. The mid-term clinical and radiological results of this operation are promising but no information about the viability of the reattached cartilage has been reported. To evaluate cartilage viability and quality after trochleoplasty and to verify the healing process, two osteochondral biopsies were harvested from three patients 6, 8, and 9 months after trochleoplasty. One cylinder was evaluated histologically to assess cartilage, calcified cartilage (cc), and subchondral bone quality, while the other one was examined by confocal microscopy to evaluate cell viability. The histological examination showed a normal matrix and cell distribution of the cartilage, while the cc showed lacunae ingrowing from the underlying bone. The subchondral bone showed normal lamellae and histology, and the healing of the flap. Confocal microscopy showed almost exclusively viable chondrocytes. This demonstration of non-injured cartilage at short-term follow-up together with promising clinical and radiological 2- and 5-year follow-up results indicate a potential promising outlook for the long term, as further chondral damage is not expected. So trochleoplasty can be seen as a primary intervention for patellar instability because of trochlear dysplasia as the risk for cartilage damage is low.
CD4CD8αα Lymphocytes, A Novel Human Regulatory T Cell Subset Induced by Colonic Bacteria and Deficient in Patients with Inflammatory Bowel Disease (2014)

How the microbiota affects health and disease is a crucial question. In mice, gut Clostridium bacteria are potent inducers of colonic interleukin (IL)-10-producing Foxp3 regulatory T cells (Treg), which play key roles in the prevention of colitis and in systemic immunity. In humans, although gut microbiota dysbiosis is associated with immune disorders, the underlying mechanism remains unknown. In contrast with mice, the contribution of Foxp3 Treg in colitis prevention has been questioned, suggesting that other compensatory regulatory cells or mechanisms may exist. Here we addressed the regulatory role of the CD4CD8 T cells whose presence had been reported in the intestinal mucosa and blood. Using colonic lamina propria lymphocytes (LPL) and peripheral blood lymphocytes (PBL) from healthy individuals, and those with colon cancer and irritable bowel disease (IBD), we demonstrated that CD4CD8αα (DP8α) T lymphocytes expressed most of the regulatory markers and functions of Foxp3 Treg and secreted IL-10. Strikingly, DP8α LPL and PBL exhibited a highly skewed repertoire toward the recognition of Faecalibacterium prausnitzii, a major Clostridium species of the human gut microbiota, which is decreased in patients with IBD. Furthermore, the frequencies of DP8α PBL and colonic LPL were lower in patients with IBD than in healthy donors and in the healthy mucosa of patients with colon cancer, respectively. Moreover, PBL and LPL from most patients with active IBD failed to respond to F. prausnitzii in contrast to PBL and LPL from patients in remission and/or healthy donors. These data (i) uncover a Clostridium-specific IL-10-secreting Treg subset present in the human colonic LP and blood, (ii) identify F. prausnitzii as a major inducer of these Treg, (iii) argue that these cells contribute to the control or prevention of colitis, opening new diagnostic and therapeutic strategies for IBD, and (iv) provide new tools to address the systemic impact of both these Treg and the intestinal microbiota on the human immune homeostasis.
Spectroscopic method for measuring refractive index (2013)

A method for routine, but precise measurements of refractive index is described. The method is fast and accurate. It is based on the analysis of interference fringes, and uses positions of the fringe maxima and/or minima and a precise measurement of sample thickness to extract refractive index. An extremely dense dataset of refractive index values over the entire spectral range of interest can be routinely obtained.
Vectorial beam shaping (2008)

An algorithm is reported for the design of a phase-only diffractive optical element (DOE) that reshapes a beam focused using a high numerical aperture (NA) lens. The vector diffraction integrals are used to relate the field distributions in the DOE plane and focal plane. The integrals are evaluated using the chirp-z transform and computed iteratively within the Method of Generalized Projections (MGP) to identify a solution that simultaneously satisfies the beam shaping and DOE constraints. The algorithm is applied to design a DOE that transforms a circularly apodized flat-top beam of wavelength lambda to a square irradiance pattern when focused using a 1.4-NA objective. A DOE profile is identified that generates a 50 lambda x 50 lambda square irradiance pattern having 7% uniformity error and 74.5% diffraction efficiency (fraction of focused power). The diffraction efficiency and uniformity decrease as the size of the focused profile is reduced toward the diffraction limited spot size. These observations can be understood as a manifestation of the uncertainty principle.
Humanized Mouse Model of Skin Inflammation Is Characterized by Disturbed Keratinocyte Differentiation and Influx of IL-17A Producing T Cells (2012)

Humanized mouse models offer a challenging possibility to study human cell function in vivo. In the huPBL-SCID-huSkin allograft model human skin is transplanted onto immunodeficient mice and allowed to heal. Thereafter allogeneic human peripheral blood mononuclear cells are infused intra peritoneally to induce T cell mediated inflammation and microvessel destruction of the human skin. This model has great potential for in vivo study of human immune cells in (skin) inflammatory processes and for preclinical screening of systemically administered immunomodulating agents. Here we studied the inflammatory skin response of human keratinocytes and human T cells and the concomitant systemic human T cell response.As new findings in the inflamed human skin of the huPBL-SCID-huSkin model we here identified: 1. Parameters of dermal pathology that enable precise quantification of the local skin inflammatory response exemplified by acanthosis, increased expression of human β-defensin-2, Elafin, K16, Ki67 and reduced expression of K10 by microscopy and immunohistochemistry. 2. Induction of human cytokines and chemokines using quantitative real-time PCR. 3. Influx of inflammation associated IL-17A-producing human CD4+ and CD8+ T cells as well as immunoregulatory CD4+Foxp3+ cells using immunohistochemistry and -fluorescence, suggesting that active immune regulation is taking place locally in the inflamed skin. 4. Systemic responses that revealed activated and proliferating human CD4+ and CD8+ T cells that acquired homing marker expression of CD62L and CLA. Finally, we demonstrated the value of the newly identified parameters by showing significant changes upon systemic treatment with the T cell inhibitory agents cyclosporine-A and rapamycin. In summary, here we equipped the huPBL-SCID-huSkin humanized mouse model with relevant tools not only to quantify the inflammatory dermal response, but also to monitor the peripheral immune status. This combined approach will gain our understanding of the dermal immunopathology in humans and benefit the development of novel therapeutics for controlling inflammatory skin diseases.
Data from Characterization of an Oxaliplatin Sensitivity Predictor in a Preclinical Murine Model of Colorectal Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Despite advances in contemporary chemotherapeutic strategies, long-term survival still remains elusive for patients with metastatic colorectal cancer. A better understanding of the molecular markers of drug sensitivity to match therapy with patient is needed to improve clinical outcomes. In this study, we used &lt;i&gt;in vitro&lt;/i&gt; drug sensitivity data from the NCI-60 cell lines together with their Affymetrix microarray data to develop a gene expression signature to predict sensitivity to oxaliplatin. To validate our oxaliplatin sensitivity signature, patient-derived colorectal cancer explants (PDCCE) were developed in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice from resected human colorectal tumors. Analysis of gene expression profiles found similarities between the PDCCEs and their parental human tumors, suggesting their utility to study drug sensitivity &lt;i&gt;in vivo&lt;/i&gt;. The oxaliplatin sensitivity signature was then validated &lt;i&gt;in vivo&lt;/i&gt; with response data from 14 PDCCEs treated with oxaliplatin and was found to have an accuracy of 92.9% (sensitivity = 87.5%; specificity = 100%). Our findings suggest that PDCCEs can be a novel source to study drug sensitivity in colorectal cancer. Furthermore, genomic-based analysis has the potential to be incorporated into future strategies to optimize individual therapy for patients with metastatic colorectal cancer. &lt;i&gt;Mol Cancer Ther; 11(7); 1500–9. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Stackelberg Voting Games: Computational Aspects and Paradoxes (2010)

We consider settings in which voters vote in sequence, each voter knows the votes of the earlier voters and the preferences of the later voters, and voters are strategic. This can be modeled as an extensive-form game of perfect information, which we call a Stackelberg voting game. We first propose a dynamic-programming algorithm for finding the backward-induction outcome for any Stackelberg voting game when the rule is anonymous; this algorithm is efficient if the number of alternatives is no more than a constant. We show how to use compilation functions to further reduce the time and space requirements. Our main theoretical results are paradoxes for the backward-induction outcomes of Stackelberg voting games. We show that for any n ≥ 5 and any voting rule that satisfies nonimposition and with a low domination index, there exists a profile consisting of n voters, such that the backward-induction outcome is ranked somewhere in the bottom two positions in almost every voter’s preferences. Moreover, this outcome loses all but one of its pairwise elections. Furthermore, we show that many common voting rules have a very low (= 1) domination index, including all majority-consistent voting rules. For the plurality and nomination rules, we show even stronger paradoxes. Finally, using our dynamic-programming algorithm, we run simulations to compare the backward-induction outcome of the Stackelberg voting game to the winner when voters vote truthfully, for the plurality and veto rules. Surprisingly, our experimental results suggest that on average, more voters prefer the backward-induction outcome.
Increased expression of beta 2-microglobulin in multidrug-resistant tumour cells (2002)

The rat monoclonal antibody LMR-12 was shown earlier to react with a plasma membrane protein, upregulated in multidrug-resistant cell lines. In this study, we observed distinct LMR-12 staining in 36 out of 55 non-drug-selected tumour cell lines, including melanomas, renal cell-, colon- and lung carcinomas, whereas in other tumour types, such as leukaemia and ovarian cancer, LMR-12 staining was generally low or absent. The cDNA encoding the LMR-12 antigen was isolated from a library of the multidrug-resistant human fibrosarcoma cell line HT1080/DR4 by expression cloning in MOP8 cells. Sequence analysis showed that the LMR-12 antigen is identical to the major histocompatibility complex class I molecule beta 2-microglobulin (beta2-m). The LMR-12/ beta2-m staining results were confirmed by mRNA microarray data from an independent National Cancer Institute study, as well as by newly obtained reverse transcriptase polymerase chain reaction data. Further analysis of the microarray data showed that beta2-m levels closely reflected levels of major histocompatibility complex class I heavy chains and the transporter associated with antigen processing. Since the ABC transporter associated with antigen processing was previously shown to contribute to multidrug-resistance, it may very well be that the observed LMR-12/ beta2-m levels are secondary to (elevated) levels of the transporter associated with antigen processing. A perspective arising from the present study is that drug resistant tumour cells may, by having elevated levels of major histocompatibility complex related molecules, be particular good candidates for alternative therapeutic therapies, such as cytotoxic T cell mediated immune-therapies.
IMine: Index Support for Item Set Mining (2008)

This paper presents the IMine index, a general and compact structure which provides tight integration of item set extraction in a relational DBMS. Since no constraint is enforced during the index creation phase, IMine provides a complete representation of the original database. To reduce the I/O cost, data accessed together during the same extraction phase are clustered on the same disk block. The IMine index structure can be efficiently exploited by different item set extraction algorithms. In particular, IMine data access methods currently support the FP-growth and LCM v.2 algorithms, but they can straightforwardly support the enforcement of various constraint categories. The IMine index has been integrated into the PostgreSQL DBMS and exploits its physical level access methods. Experiments, run for both sparse and dense data distributions, show the efficiency of the proposed index and its linear scalability also for large datasets. Item set mining supported by the IMine index shows performance always comparable with, and sometimes better than, state of the art algorithms accessing data on flat file.
Supercritical Fluid Extraction of Toxic Heavy Metals from Solid and Aqueous Matrices (2003)

The feasibility of using dithiocarbamate chelating agents or sulfur-containing organophosphorus reagents for the supercritical fluid extraction (SFE) of toxic heavy metals from solid and aqueous matrices was investigated. Effective extraction of heavy metal ions from both sand matrix and water samples was demonstrated by using supercritical CO2 containing dithiocarbamate chelating agents. A commercially available sulfur-containing organophosphorus reagent, Cyanex 302, was used for the extraction of toxic heavy metals from wood samples. The extraction profiles were initially rapid followed by a very low level of metal extraction, indicating that the process is limited to extraction of leachable toxic metals.
An animat's cell doctrine. (2011)

We present a developmental model to simulate swimming digital organisms following an animat’s cell doctrine. Mor-phology and control are encoded in one genome concurrently using artificial cells as the basic building blocks for both. Each individual starts with one cell in the middle of a com-putational environment, and its development is controlled by a gene regulatory network. The cells can differentiate into central pattern generators that control the movements of the resulting individual. After the developmental process, the in-dividual is placed into a physics simulation environment and the distance it swims in a defined time is evaluated. Contrary to most existing models, one genome for both, morphology and control is used and the CPGs representing the dynamic control contribute to the morphology of the organism.
Micropatterning as a tool to decipher cell morphogenesis and functions (2010)

In situ, cells are highly sensitive to geometrical and mechanical constraints from their microenvironment. These parameters are, however, uncontrolled under classic culture conditions, which are thus highly artefactual. Micro-engineering techniques provide tools to modify the chemical properties of cell culture substrates at sub-cellular scales. These can be used to restrict the location and shape of the substrate regions, in which cells can attach, so-called micropatterns. Recent progress in micropatterning techniques has enabled the control of most of the crucial parameters of the cell microenvironment. Engineered micropatterns can provide a micrometer-scale, soft, 3-dimensional, complex and dynamic microenvironment for individual cells or for multi-cellular arrangements. Although artificial, micropatterned substrates allow the reconstitution of physiological in situ conditions for controlled in vitro cell culture and have been used to reveal fundamental cell morphogenetic processes as highlighted in this review. By manipulating micropattern shapes, cells were shown to precisely adapt their cytoskeleton architecture to the geometry of their microenvironment. Remodelling of actin and microtubule networks participates in the adaptation of the entire cell polarity with respect to external constraints. These modifications further impact cell migration, growth and differentiation.
In Vitro Inhibition of Phosphodiesterase 3B (PDE 3B) by Anthocyanin-Rich Fruit Juice Extracts and Selected Anthocyanins (2020)

Phosphodiesterases (PDEs) are essential enzymes for the regulation of pathways mediated by cyclic adenosine monophosphate (cAMP). Secondary plant compounds like anthocyanins (ACs) can inhibit PDE activity and, consequently, may be beneficial for lipid metabolism. This study investigated 18 AC-rich juice extracts and pure reference compounds from red fruits for potential inhibitory effects on PDE 3B activity. Extracts were obtained through adsorption on Amberlite<sup>®</sup> XAD 7 resin. Based on this screening, the chokeberry, blueberry, pomegranate, and cranberry extracts were active, with half maximal inhibitory concentrations (IC<sub>50</sub>) ranging from 163 ± 3 µg/mL to 180 ± 3 µg/mL. The ACs in these extracts, peonidin-3-glucoside and cyanidin-3-arabinoside, were the most active single compounds (IC<sub>50</sub> = 56 ± 20 µg/mL, 108 ± 6 µg/mL). All extracts comprised high amounts of phenolic compounds, as determined by the Folin-Ciocalteu assay, ranging from 39.8 ± 1.5 to 73.5 ± 4.8 g gallic acid equivalents (GAE)/100 g extract. Pomegranate and chokeberry extracts exhibited the largest amounts of polyphenols (72.3 ± 0.7 g GAE/100 g, 70.6 ± 4.1 g GAE/100 g, respectively). Overall, our results showed that fruit juice extracts and their ACs can inhibit PDE activity. Any potential health benefits in vivo will be investigated in the future.
Medical Perspective Articles to Stimulate the Field for Needs-Finding (2018)

This editorial by the journal's Editor in Chief, Brian Pogue, explains the need for a new type of paper.
Expression of macrophage inflammatory protein-2 and KC mRNA in pulmonary inflammation. (1992)

This study sought to test the hypothesis that expression of mRNA for two cytokines, macrophage inflammatory protein-2 (MIP-2) and the KC gene product, is induced in rat lung cells during inflammatory responses in vitro and in vivo. Macrophage inflammatory protein-2 and KC are members of the platelet-factor 4 (PF-4) cytokine superfamily that cause marked neutrophil chemotaxis and activation in vitro. To investigate expression of the genes for MIP-2 and KC in rat models of lung injury, cDNA probes for these cytokines in the rat were made from polymerase chain reaction (PCR) products generated using mouse sequence-derived primers. Sequence analysis of these cDNAs showed marked homology to known murine sequences (89% and 92% MIP-2 and KC, respectively). These cDNAs were first used to study the expression of these two genes in rat alveolar macrophages (AMs) in vitro by Northern blot hybridization. Lipopolysaccharide (LPS) treatment of rat AMs in vitro caused marked increases in mRNA for both KC and MIP-2 within 30 minutes, which persisted through the 6 hours measured. To study expression during inflammation in vivo, rats were treated with LPS by intratracheal instillation. Bronchoalveolar lavage (BAL) cells and whole trachea homogenates were analyzed. There was a marked and rapid increase in MIP-2 and KC mRNA levels within both BAL cells and trachea homogenates after LPS instillation. The results support the hypothesis that MIP-2 and KC cytokines contribute to neutrophil chemotaxis and activation in this rat model of acute pulmonary inflammation.
The Network of Cytokines in Brain Metastases (2021)

Brain metastases are the most common of all intracranial tumors and a major cause of death in patients with cancer. Cytokines, including chemokines, interferons, interleukins, lymphokines, and tumor necrosis factors are key regulators in the formation of brain metastases. They regulate the infiltration of different cellular subsets into the tumor microenvironment and affect the therapeutic outcomes in patients. Elucidating the cancer cell-cytokine interactions in the setting of brain metastases is crucial for the development of more accurate diagnostics and efficacious therapies. In this review, we focus on cytokines that are found in the tumor microenvironment of brain metastases and elaborate on their trends of expression, regulation, and roles in cellular recruitment and tumorigenesis. We also explore how cytokines can alter the anti-tumor response in the context of brain metastases and discuss ways through which cytokine networks can be manipulated for diagnosis and treatment.