gebhart/patrepeval huggingface dataset:
Human breast cancer metastases to the brain display GABAergic properties in the neural niche (2014)

Dispersion of tumors throughout the body is a neoplastic process responsible for the vast majority of deaths from cancer. Despite disseminating to distant organs as malignant scouts, most tumor cells fail to remain viable after their arrival. The physiologic microenvironment of the brain must become a tumor-favorable microenvironment for successful metastatic colonization by circulating breast cancer cells. Bidirectional interplay of breast cancer cells and native brain cells in metastasis is poorly understood and rarely studied. We had the rare opportunity to investigate uncommonly available specimens of matched fresh breast-to-brain metastases tissue and derived cells from patients undergoing neurosurgical resection. We hypothesized that, to metastasize, breast cancers may escape their normative genetic constraints by accommodating and coinhabiting the neural niche. This acquisition or expression of brain-like properties by breast cancer cells could be a malignant adaptation required for brain colonization. Indeed, we found breast-to-brain metastatic tissue and cells displayed a GABAergic phenotype similar to that of neuronal cells. The GABAA receptor, GABA transporter, GABA transaminase, parvalbumin, and reelin were all highly expressed in breast cancer metastases to the brain. Proliferative advantage was conferred by the ability of breast-to-brain metastases to take up and catabolize GABA into succinate with the resultant formation of NADH as a biosynthetic source through the GABA shunt. The results suggest that breast cancers exhibit neural characteristics when occupying the brain microenvironment and co-opt GABA as an oncometabolite.
FTOS-Verify: Analysis and Verification of Non-Functional Properties for Fault-Tolerant Systems (2009)

The focus of the tool FTOS is to alleviate designers' burden by offering code generation for non-functional aspects including fault-tolerance mechanisms. One crucial aspect in this context is to ensure that user-selected mechanisms for the system model are sufficient to resist faults as specified in the underlying fault hypothesis. In this paper, formal approaches in verification are proposed to assist the claim. We first raise the precision of FTOS into pure mathematical constructs, and formulate the deterministic assumption, which is necessary as an extension of Giotto-like systems (e.g., FTOS) to equip with fault-tolerance abilities. We show that local properties of a system with the deterministic assumption will be preserved in a modified synchronous system used as the verification model. This enables the use of techniques known from hardware verification. As for implementation, we develop a prototype tool called FTOS-Verify, deploy it as an Eclipse add-on for FTOS, and conduct several case studies.
Dynamic Conceptional Contrastive Learning for Generalized Category Discovery (2023)

Generalized category discovery (GCD) is a recently proposed open-world problem, which aims to automatically cluster partially labeled data. The main challenge is that the unlabeled data contain instances that are not only from known categories of the labeled data but also from novel categories. This leads traditional novel category discovery (NCD) methods to be incapacitated for GCD, due to their assumption of unlabeled data are only from novel categories. One effective way for GCD is applying self-supervised learning to learn discriminate representation for unlabeled data. However, this manner largely ignores underlying relationships between instances of the same concepts (e.g., class, super-class, and sub-class), which results in inferior representation learning. In this paper, we propose a Dynamic Conceptional Contrastive Learning (DCCL) framework, which can effectively improve clustering accuracy by alternately estimating underlying visual conceptions and learning conceptional representation. In addition, we design a dynamic conception generation and update mechanism, which is able to ensure consistent conception learning and thus further facilitate the optimization of DCCL. Extensive experiments show that DCCL achieves new state-of-the-art performances on six generic and fine-grained visual recognition datasets, especially on fine-grained ones. For example, our method significantly surpasses the best competitor by 16.2% on the new classes for the CUB-200 dataset. Code is available at https://github.com/TPCD/DCCL.
P3-17-11: Dovitinib (TKI258), a Dual Inhibitor of FGFR and VEGFR, Induces Tumor Growth Suppression in Xenograft Models of Primary Human Breast Cancer. (2011)

Abstract Introduction: The objective of this study was to evaluate the efficacy of dovitinib (TKI258), a small-molecule dual inhibitor of fibroblast growth factor receptor (FGFR) and vascular endothelial growth factor receptor (VEGFR) in mouse models of human breast cancer. Molecular epidemiological studies have implicated that FGFR1 and FGFR2 gene amplification plays a critical role in breast cancer tumorigenesis. FGFR1 gene amplification correlates with gene expression and is associated with poor prognosis in patients with estrogen receptor-positive (ER+) tumors. Dual FGFR/VEGFR inhibitory activities of dovitinib make it an attractive molecule for targeting breast cancer. Experimental Design: Dovitinib was evaluated in 3 primary human breast carcinoma xenograft models with different histological and molecular profiles: a triple-negative breast cancer model (HBCx-15), a HER2+ model (HBCx-5), and an ER+ model (HBCx-3). Dovitinib was administered orally at 20- and 40-mg/kg dose levels (n = 8–10/group), once daily for 21 consecutive days. Results: At a dose of 40 mg/kg, dovitinib demonstrated strong antitumor efficacy as a single agent, particularly in the ER+ HBCx-3 and the HER2+ BCx-5 tumor models (ΔT/T0 = −26.42% and ΔT/ΔC = 5.09%, respectively), whereas the response was less significant in the triple negative breast cancer HBCx-15 model (ΔT/ΔC = 31.7%). Conclusion: Dovitinib showed significant antitumor effect in human breast cancer xenograft mouse models. This study provides a strong rationale for clinical investigation of dovitinib in patients with advanced breast cancer, particularly in patients with ER+ and HER2+ disease. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-17-11.
Supplementary Figure S2 from A miRNA-Based Signature Detected in Primary Melanoma Tissue Predicts Development of Brain Metastasis (2023)

&lt;p&gt;Supplementary Figure S2. This figure depicts brain metastatsis-free and overall survival, as plotted kaplan-meier survival curves, of high- vs low-risk patients (determined by the miRNA signature + stage model) for patients stratified by stage at diagnosis.&lt;/p&gt;
Design and analysis of dual-axis rotating scheme for ring laser strapdown inertial navigation system (2016)

Error rotating compensation method can effectively improve the long-time navigation accuracy. The rotation program of the turntable is an important factor to determine the precision of rotary strapdown inertial navigation system. By deriving the error model of strapdown inertial navigation system and analyzing the navigation propagating function, the mechanism of error rotating compensation is described in detail. And the propagation characteristics of inertial sensor error, scale factor error and installation error are also studied. Based on the dual-axis rotating strapdown inertial navigation system, a thirty-two sequence indexing scheme is put forward to modulate the inertial instrument errors better. The simulation results show that the thirty-two sequence dual-axis indexing scheme can effectively reduce the amplitude of the errors. And it has obvious advantages when compared with the sixteen sequence dual-axis indexing scheme.
RSA Public Key Validation (2001)

With increasing demands for internet security, the demand for distribution of public key certificates and certificate authorities spreads. This brings up the new problem of public key validation. This problem can arise in different contexts and can be adressed in some of them using novel zero knowledge protocols, while in other contexts it can be only poorly solved. The purpose of this paper is to give an overview of the topic of key validation and to discuss the possible solutions to the different instances in which it appears. We also present a new zero knowledge protocol for correctness of an RSA public exponent and a simple protocol (not zero-knowledge) for primality of a discrete logarithm. We use the latter to give a proof protocol (not zero knowledge) that an RSA key is the product of strong primes
Development of an Effective Cryopreservation Protocol for Blue Catfish Oogonia (2021)

Abstract Long-term storage of oogonia and germ-line stem cells provides an alternative to the limitations associated with cryopreserving eggs of important fish species. These cell types are less vulnerable to the stresses of freezing. Cryopreservation has enormous potential for aquaculture advancement, but protocols must be developed for each species and cell type since its success hinges on various input factors. Blue Catfish Ictalurus furcatus were selected as the test species in this study because of the need to improve fry production of Blue Catfish ♂ × Channel Catfish I. punctatus ♀ hybrids, which can be facilitated by storing oogonia in gene banks. Our objective was to develop a freezing protocol for oogonia of this species. We tested different permeating and nonpermeating cryoprotectants, concentrations of these agents, and freezing rates. We proved that all three factors influenced postthaw recovery of oogonia. Of the permeating cryoprotectants, 1.0 M dimethyl sulfoxide resulted in the most live cells with the highest viability percentages, and adding 0.2 M lactose with 10% egg yolk further improved the results. There were also specific interactions in which the effects of concentration and freezing rate varied among the cryoprotectant treatments. The most effective freezing rate was −1.0°C/min, and cell viability was reduced at −2.5°C/min and −5.0°C/min. From these results, we propose adding 1.0 M dimethyl sulfoxide with 0.2 M lactose and 10% egg yolk to cryomedia and freezing it at a rate of −1.0°C/min. By developing a cryopreservation protocol for a commonly cultured catfish, this work may guide the development of protocols for other species of interest.
Diabetic Wound Imaging Using a Noncontact Near-Infrared Scanner (2015)

An estimated 15% of all patients suffering with diabetes will develop foot ulcers.1 To date, clinicians employ visual inspection of the wound site during its standard 4-week healing process via monitoring of surface granulation. However, surface granulation is not an implication of internal healing in many cases. If left untreated immediately, the extent of leg/foot amputation may increase due to lack of response to the treatment.

Near-infrared spectroscopy (NIRS) is an emerging noninvasive and nonionizing technology that can map the changes in hemodynamics in the site of interest (eg, the wounded and healthy tissue site) even up to a few centimeters deep. Researchers have implemented NIRS toward wound healing studies in animals and pilot human subject studies as well.2-3 Herein, a near-infrared optical scanner (NIROS) is implemented in differentiating healing/nonhealing foot ulcers.

NIROS was set up to image large tissue surfaces (>12 cm2) without contact using an LED-based source and an NIR sensitive camera (IDS, Germany). A custom-developed imaging software is used to acquire diffuse reflected NIR images in real time from the tissue surface. IRB-approved imaging studies were carried out on 4 diabetic subjects with wounds at Somesh’s Diabetic Foot Clinic, Chennai, India (www.ndiabeticfoot.com). Diffuse reflected optical images were acquired from the wound and its surrounding regions in all subjects. The optical contrast of wound:peripheries was estimated from the intensity distribution in the wound with respect to its peripheries. From the qualitative and quantitative analysis, it was observed that there is a negative wound:background optical contrast in nonhealing wounds (see Figures 1a and ​and1c)1c) compared to a positive wound:background contrast in healing wounds (see Figures 1b and ​and1d).1d). Healing wounds initially have a higher hemoglobin concentration in the wound site, and with time (in weeks) they tend to decrease and become closer to the hemoglobin concentrations of the normal background.2-3 On the contrary, nonhealing wounds have a higher hemoglobin concentration that does not decrease with time due to the chronic inflammatory phase of these wounds. Extent of absorption of NIR light is directly proportional to hemoglobin concentration. Hence, a negative optical contrast potentially indicates a greater hemoglobin concentration in the wound site with respect to the surroundings than a healing wound that progressed to cell proliferation stage (where hemoglobin is consumed). Thus, a biometric of positive and negative optical contrast is shown to differentiate healing and nonhealing wounds, with future emphasis on extensive studies to validate the results.



Figure 1.

Near-infrared optical images of diabetic subjects with healing or nonhealing ulcers. The plots in third column correspond to the zoomed out region of interest with the intensity profile at a chosen y-plane. The intensity varies from max to min along the ...
Optimum Development of a Thin Box-Shaped Reservoir with Multiply Fractured Horizontal Wells (1998)

Abstract Very low permeability reservoirs are commonly developed with hydraulically fractured wells. Quite often, drilling costs must be reduced and/or the number of slots on an offshore platform is limited. Vertical wells are then replaced by a horizontal well with a set of parallel, equal size hydraulic fractures. A recurrent question concerns the productivity index of this multiply fractured horizontal well. Simple analytical expressions of this index have been provided by Mukherjee et al.1 and later corrected by Lietard et al.2 They however underestimate to a large extent the actual performance of this type of well. The present paper proposes a much better definition of the productivity index of multiply fractured wells. It is based on the usage of Dietz’ shape factors3 for vertical wells centered in independent box-shaped drainage areas of equal size in the considered reservoir. For this purpose, Gringarten’s work4 about shape factors for hydraulically fractured wells has been revisited, and corrected equations are presented in this paper.
The BINGO! System for Information Portal Generation and Expert Web Search (2003)

This paper presents the BINGO! focused crawler, an advanced tool for information portal generation and expert Web search. In contrast to standard search engines such as Google which are solely based on precomputed index structures, a focused crawler interleaves crawling, automatic classification, link analysis and assessment, and text filtering. A crawl is started from a user-provided set of training data and aims to collect comprehensive results for the given topics.
Confirmation of Piscirickettsia salmonis as a pathogen in European sea bass Dicentrarchus labrax and phylogenetic comparison with salmonid strains (2005)

European sea bass Dicentrarchus labrax from the Mediterranean were diagnosed with a severe encephalitis. Rickettsia-like organisms (RLOs) were associated with brain lesions in routine paraffin sections. These were found to share common antigens with the Piscirickettsia salmonis type-strain, LF-89, by indirect fluorescent antibody test (IFAT) and by immunohistochemistry (IHC). In addition, we compared the DNA sequences of the 16S rDNA and 16S-23S internal transcribed spacer region (ITS) with those published for P. salmonis strains and found that the sea bass piscirickettsia-like organism (SBPLO) was another strain of P. salmonis, closely related to the salmonid pathogens. Furthermore, we showed that the SBPLO possessed at least 2 ITS regions, 1 of which contained tRNA genes.
Impact of 68Ga-PSMA-11 PET on the management of biochemically recurrent prostate cancer in a prospective single-arm clinical trial. (2020)

292 Background: Prostate-specific membrane antigen ligand positron emission tomography (PSMA PET) induced management changes in up to every second patient in smaller clinical trials. We aim to determine the impact of 68 Ga-PSMA-11 PET/CT on management of biochemically recurrent prostate cancer in a large prospective cohort. Methods: We report management changes following PSMA PET, a secondary endpoint of a prospective multicenter trial in men with prostate cancer biochemical recurrence (NCT02940262 and NCT03353740). Pre-PET, Post-PET and Post-Treatment Questionnaires were sent to referring physicians recording working clinical summaries, intended and implemented therapeutic and diagnostic management. Results: Intended management change occurred in 260/382 (68%) patients. Intended change was considered major in 176/382 (46%) patients. Management pathway aligned with PET findings, i.e. change towards local/focal therapy for locoregional disease (54/126 patients, 44%) and towards systemic therapy or combination approaches for metastatic disease (106/153 patients, 69%). Intended management was implemented in 160/206 (78%) patients. Perceived site of disease was unknown in 259/382 (68%) patients before and 111/382 (29%) patients after PSMA PET. A total of 150 intended diagnostic tests, mostly CT (n=43, 29%) and bone Scans/NaF-PET (n=52, 35%), were prevented by PSMA PET. A total of 73 tests, mostly biopsies (n=44, 60%) requested by the study protocol, were triggered. Conclusions: Disease localization by PSMA PET translated into management changes in more than half of patients with biochemical recurrence of prostate cancer. More than twice as many diagnostic tests were prevented than triggered following PET. Clinical trial information: NCT02940262 and NCT03353740.
Velocity Distribution and Dip-Phenomenon in Smooth Uniform Open Channel Flows (2004)

This paper investigates the mechanism of the dip phenomenon whereby the location of the maximum velocity appears below the free surface vis-à-vis the secondary currents in open-channel flows. It is found that the classical log law gives a good description of the velocity distribution in the inner region if the local shear velocity is introduced into the dimensionless distance, i.e., u*(z)y/ν. In the outer region, where the maximum velocity occurs at some distance below the free surface in a vertical plane, it is found that the velocity deviation from the log law is linearly proportional to the logarithmic distance ln(1-y/h) from the free surface. To this end, the study proposes a dip-modified log law for the velocity distribution in smooth uniform open channel flows. This new law is capable of describing the dip phenomenon, and is applicable to the velocity profile in the region from the near bed to just below the free surface, and transversely, from the center line to the near-wall region of the channel. The dip-modified log law consists of two logarithmic distances, one from the bed ln(u*(z)y/ν), and the other from the free surface ln(1-y/h), respectively, and a dip-correction factor α. The latter is the only parameter that needs to be determined and an empirical equation for α has been proposed in this study. The dip-modified log law has been verified using published experimental data for smooth rectangular open channels and the agreement between the measured and computed velocity profiles is good.
Characterization of Dislocations and Micropipes in 4H n<sup>+</sup> SiC Substrates (2008)

Etching of 4H-SiC wafers in molten KOH as a method for micropipe and dislocation density analysis was investigated. The obtained results were correlated with those of the synchrotron white beam x-ray topography. Heavily nitrogen-doped SiC shows a significantly different etching behavior in comparison with the low-doped material. This complicates identification of different types of threading defects. In particular, it is difficult to separate Threading Screw Dislocations (TSD) from Threading Edge Dislocations (TED). Depending on the level of doping and thermal history of the crystal, some of the etch pits emerging due to the 1c screw dislocations can be as large as those due to the micropipes.
Simulation of developing human neuronal cell networks (2016)

To conclude, our model reflects the assumption that the interaction between excitatory and inhibitory neurons during the maturation of a neuronal network and the spontaneous emergence of bursts are due to increased connectivity caused by the forming of new synapses.
Role of antiapoptotic STAT3 and BCL-2 signaling in promoting lung tumor cells to survive against combined MET-/EGFR-targeted inhibitors. (2010)

10644 Background: Epidermal growth factor receptor (EGFR) inhibitors in lung cancer are largely limited by the development of resistant disease that ultimately limits their clinical utility. Combined targeted therapy strategies using both MET and EGFR small molecular tyrosine kinase inhibitors (TKIs) are under preclinical and clinical investigation to enhance the therapeutic efficacy and to circumvent acquired EGFR TKI resistance in lung cancer. These combined therapeutic approaches are likely to have unique mechanisms of resistance. Methods: We investigated the effects of combined MET/EGFR TKI treatment on signal transducer and activator of transcription 3 (STAT3) and B-cell lymphoma protein 2 (BCL-2) family members in lung cancer cell lines and xenografts models that are resistant to EGFR inhibitors. Results: Activated STAT3 and BCL-2/BCL-XL induction were seen in lung tumor cells that survived targeted inhibition by MET kinase inhibitors (SU11274 and PHA665752), either alone or in combination with EGFR inhibitors. Using in vivo xenograft model with luciferase-expressing H1975 cells for bioluminescence imaging (BLI), we show that while the H1975 xenograft exhibited excellent imaging tumor response when treated with combined SU11274 (MET TKI) and erlotinib (EGFR TKI), activated P-STAT3[Y705] expression was evident in the residual microscopic tumor survivor cells within the treated xenograft. Interestingly, the resistant survivor tumor cells were located predominantly along the peripheral rind juxtaposing the host stroma. BCL-2 expression was also found induced in the tumor survivor cells during the course of targeted combined MET/EGFR inhibition in vivo. Conclusions: Results of our study support the role of activated STAT3, and its downstream transcriptional targets of the antiapoptotic BCL-2 family members as potential markers for tumor resistance against combined MET/EGFR targeted inhibitors in lung cancer. Further investigations to target the intrinsic apoptotic pathway with BCL-2 family inhibitors, which may overcome or prevent resistance against combined MET/EGFR TKIs, are warranted to impact on the long term outcome in lung cancer therapy. No significant financial relationships to disclose.