gebhart/patrepeval huggingface dataset:
Yesterday's weather: guiding early reverse engineering efforts by summarizing the evolution of changes (2004)

Knowing where to start reverse engineering a large software system, when no information other than the system's source code itself is available, is a daunting task. Having the history of the code (i.e., the versions) could be of help if this would not imply analyzing a huge amount of data. We present an approach for identifying candidate classes for reverse engineering and reengineering efforts. Our solution is based on summarizing the changes in the evolution of object-oriented software systems by defining history measurements. Our approach, named Yesterday's Weather, is an analysis based on the retrospective empirical observation that classes which changed the most in the recent past also suffer important changes in the near future. We apply this approach on two case studies and show how we can obtain an overview of the evolution of a system and pinpoint its classes that might change in the next versions.
Epidermal growth factor receptor and caveolin-1 coexpression identifies adult supratentorial ependymomas with rapid unfavorable outcomes (2010)

Supratentorial ependymomas account for a minority of intracranial ependymomas, which still have uncertain prognostic markers. Among them, epidermal growth factor receptor (EGFR) overexpression correlates with a poor prognosis. In glioblastoma cells, EGFR function has been reported to be regulated by its migration from cell membrane infoldings called caveolae and by its colocalization with the caveolae-associated protein caveolin-1 (cav-1). Therefore, we decided to investigate cav-1 expression and coexpression with EGFR in a series of adult intracranial ependymomas. We analyzed 22 adult supratentorial ependymomas and compared tumor grades as determined by the WHO classification and patient survival rates with the expression of EGFR, cav-1, and p53 and the values of the proliferation marker Ki-67, all tested by immunohistochemistry; in addition, we investigated the mutational profile of cav-1. The results demonstrate that the tumor grade is directly correlated with EGFR, Ki-67, and cav-1 expression only, whereas (by univariate analysis) the expression of all the studied markers, as well as the tumor histological grade, significantly correlated with the patient's overall survival (OS). By multivariate analysis using the Cox proportional hazards model, among all variables considered, cav-1 was the only independent prognostic marker related to OS (relative risk = 13.92; P = .013). Among grade II ependymomas, only cav-1 correlated with poor OS (P = .011), distinguishing 2 distinct subgroups of tumors with different outcomes despite sharing identical grading. All the patients studied carried wild-type cav-1 sequences, demonstrating that cav-1 overexpression is not driven by activating mutations, as previously reported in other tumor types. Interestingly, after stratifying all cases into 4 distinct groups according to cav-1 and EGFR expression (cav-1+/EGFR+, cav-1-/EGFR-, cav-1+/EGFR-, and cav-1-/EGFR+), the coexpression of cav-1 and EGFR identified a subset of patients with definitively poor prognoses. Further studies are needed to support this evidence on a larger scale and to clarify how cav-1 and EGFR interaction can influence tumor aggressiveness.
Mercury droplet microswitch for re-configurable circuit interconnect (2004)

With electrostatic actuation, mercury droplets can act as moving and contact parts in a microswitch system. The physical stability of droplets in microscale and the low contact resistance between liquid and solid make the mercury switch an excellent candidate for the re-configurable circuit interconnect. Unlike previous micro-droplet switches, this paper reports, for the first time, a planar design and fabrication be compatible with underlying CMOS circuits. The driving voltage of the device is reduced from more than 150 V to around 80 V by surface modification technology. The response time for the switching is less than 1ms.
Cordless batteryless wheel mouse application utilizing radio requestable SAW devices in combination with the giant magneto-impedance effect (2001)

Surface acoustic wave devices for wireless identification (ID) systems, the so-called ID tags, can be turned into novel sensor elements (transponders) for impedance sensors by making use of magnetic-field variations caused by the wheel rotation and key-click functionality of a personal computer (PC) mouse. This kind of sensor does not need any power supply and may be interrogated wirelessly. Interdigital transducers are used as loadable reflectors, while another fixed reflector is used as reference to compensate cross sensitivity for temperature, mechanical stress, etc. The load of the reflectors influences amplitude and phase of the reflected wave. The load's impedance is changed utilizing the giant magneto-impedance (GMI) effect in a 30-/spl mu/m-diameter amorphous FeCoSiNd wire of zero magnetostriction. The measurand, represented by the PC-mouse key clicks and wheel rotation, influences a magnetic field, which varies the impedance of the GMI wire. Consequently, the load of the reflector influences the reflected acoustic wave and the response signal of the radio sensor. The operating principle of such a magnetic-field sensor is discussed, and the tuning for an application in a passive and cordless PC mouse is presented.
Disseminated Infection After Bacille Calmette‐Guérin Instillation for Treatment of Bladder Carcinoma (1999)

Intravesical instillations of bacille Calmette-Gue rin (BCG), an attenuated organism derived from the bovine tubercle bacillus Mycobacterium bovis, are frequently accompanied by local side effects, but adverse systemic reactions occur in 3%-5% of patients We describe two patients who developed, after intravesical instillation of BCG, pancytopenia associated with mycobacterial infection and well-formed granulomas in bone marrow biopsy specimens.
Blue-green laser diodes (1991)

The first laser diodes fabricated from wide-band-gap II-VI semiconductors are demonstrated. These devices emit coherent light at a wavelength of 490 nm from a ZnSe-based single-quantum-well structure under pulsed current injection at 77 K. This is the shortest wavelength ever generated by a semiconductor laser diode.
Models and issues in data stream systems (2002)

In this overview paper we motivate the need for and research issues arising from a new model of data processing. In this model, data does not take the form of persistent relations, but rather arrives in multiple, continuous, rapid, time-varying data streams. In addition to reviewing past work relevant to data stream systems and current projects in the area, the paper explores topics in stream query languages, new requirements and challenges in query processing, and algorithmic issues.
Human Oncogenic Viruses and Cancer (2014)

The role of viral infection in cancer was established towards the beginning of 20th century. The study of tumour viruses, their oncogenes and different mechanisms employed by these viruses to subvert the growth-suppressive and pro-apoptotic functions of host tumour suppressor genes has laid the foundation of cancer biology. The human tumour viruses induce malignancies after a prolonged latency and in conjunction with other environmental and host factors. The eight known human tumour viruses contribute to nearly 10-15% of the cancers worldwide. Advancements in research on virus-related cancers offer a plethora of opportunities to fight cancer by preventing viral spread through vaccination and use of antivirals. Besides, recent developments on viral oncogenic mechanisms should allow development of novel and targeted approaches for control and treatment of virus-associated human cancers.
The Effects of Strontium Ranelate on the Risk of Vertebral Fracture in Women with Postmenopausal Osteoporosis (2004)

Treatment of postmenopausal osteoporosis with strontium ranelate leads to early and sustained reductions in the risk of vertebral fractures.
The Pharmacology of Aldose Reductase Inhibitors (1985)

Due to the massive data sets available for drug candidates, modern drug discovery has advanced to the big data era. Central to this shift is the development of artificial intelligence approaches to implementing innovative modeling based on the dynamic, ...Read More
Differential Reactivity of Germ Line Allelic Variants of a Broadly Neutralizing HIV-1 Antibody to a gp41 Fusion Intermediate Conformation (2011)

Genetic factors, as well as antigenic stimuli, can influence antibody repertoire formation. Moreover, the affinity of antigen for unmutated naïve B cell receptors determines the threshold for activation of germinal center antibody responses. The gp41 2F5 broadly neutralizing antibody (bNAb) uses the V(H)2-5 gene, which has 10 distinct alleles that use either a heavy-chain complementarity-determining region 2 (HCDR2) aspartic acid (D(H54)) or an HCDR2 asparagine (N(H54)) residue. The 2F5 HCDR2 D(H54) residue has been shown to form a salt bridge with gp41 (665)K; the V(H)2-5 germ line allele variant containing N(H54) cannot do so and thus should bind less avidly to gp41. Thus, the induction of 2F5 bNAb is dependent on both genetic and structural factors that could affect antigen affinity of unmutated naïve B cell receptors. Here, we studied allelic variants of the V(H)2-5 inferred germ line forms of the HIV-1 gp41 bNAb 2F5 for their antigen binding affinities to gp41 linear peptide and conformational protein antigens. Both V(H)2-5 2F5 inferred germ line variants bound to gp41 peptides and protein, including the fusion intermediate protein mimic, although more weakly than the mature 2F5 antibody. As predicted, the affinity of the N(H54) variant for fusion-intermediate conformation was an order of magnitude lower than that of the D(H54) V(H)2-5 germ line antibody, demonstrating that allelic variants of 2F5 germ line antibodies differentially bind to gp41. Thus, these data demonstrate a genetically determined trait that may affect host responses to HIV-1 envelope epitopes recognized by broadly neutralizing antibodies and has implications for unmutated ancestor-based immunogen design.
Changes in serum concentrations of matrix metalloproteinases, tissue inhibitors of metalloproteinases and type IV collagen in patients with various types of glomerulonephritis. (1997)

One of the major causes of glomerular sclerosis which precedes renal failure is an increase in glomerular extracellular matrices (ECMs). Glomerular ECMs which are composed of mesangial matrix and basement membrane play an important role in physical, mechanical and structural functions of the glomerulus. Matrix metalloproteinases (MMPs) are the enzymes which degrade both the collagenous and noncollagenous components of the ECMs. Tissue inhibitors of metalloproteinases (TIMPs) are inhibitors of MMPs. The regulations by MMPs and TIMPs are considered to contribute to maintain homeostasis in the production and degradation of ECMs in the glomeruli. In the glomeruli of patients with glomerulonephritis, the imbalance between production and degradation of ECMs is supposed to cause the increase in ECMs and glomerular sclerosis. In this study, serum concentrations of MMP-1, -2, and -3, TIMP-1 and 2 and type IV collagen were measured in patients with IgA nephropathy, lupus nephritis and membranous nephropathy. In patients with IgA nephropathy and lupus nephritis which are mesangial proliferative glomerulonephritis, the levels of MMP-3 and TIMP-2 were increased. On the other hand, the levels of type IV collagen, MMP-2 and TIMP-1 were increased in patients with membranous nephropathy in which the thickening of basement membrane is characteristic. These differences may be caused by the difference of the pathogenesis of these diseases. The present results suggest that the imbalance between the metabolism of ECMs occurs in patients with glomerulonephritis and contributes to the progression of glomerulonephritis.
Regulation of Ca(2+)-activated K+ channels in pulmonary vascular smooth muscle cells: role of nitric oxide (1996)

Nitric oxide (NO.) is believed to mediate nitrovasodilators and acetylcholine-induced vasodilatation via increasing intracellular guanosine 3',5'-cyclic monophosphate (cGMP) levels. The cellular mechanisms involved in No.-mediated pulmonary vasodilatation are complex and include membrane hyperpolarization. Using the patch-clamp technique in cell-attached and inside-out configurations, we examined the effect of NO. gas, 3-morpholinosydnomimine hydrochloride (SIN-1), and perfusate from ACh-stimulated human pulmonary arterial endothelial cells, or endothelium-derived relaxing factors (EDRF), on the Ca(2+)-dependent K+ (KCa) channels in isolated cultured human pulmonary arterial smooth muscle cells (HPSMC). NO., SIN-1, and EDRF caused similar increases in KCa channel activity. Inhibiting cGMP generation with methylene blue or inhibiting the effect(s) of cGMP with the cGMP antagonist 8-bromoguanosine 3',5'-cyclic monophosphorothioate Rp isomer Rp-cGMPS prevented the NO.- and SIN-1-mediated activation of KCa channels, respectively. Treating the human pulmonary arterial endothelial cells with methylene blue blocked the EDRF-mediated activation of KCa channels in HPSMC. The cGMP analogue 8-bromo-cGMP increased KCa channel activity in intact cells and in excised inside-out HPSMC membrane patches. In the presence of cGMP and ATP, the alpha-isozyme of the cGMP-dependent protein kinase (I alpha-cGMP-PK) significantly increased KCa channel activity, and the channel activation was further increased on addition of the protein phosphatase inhibitors okadaic acid and calyculin A. Furthermore, the cGMP-mediated KCa channel activation was reduced by the cyclic nucleotide-dependent protein kinase inhibitor N-[2-methylamino)ethyl]-5-isoquinlinesulfonamide (H-8). Thus, in HPSMC, the mechanism of NO.- and native EDRF-induced KCa channel activation appears to be mediated via cGMP-I alpha-cGMP-PK phosphorylation of KCa channels.
Regional Cerebral Hyperperfusion and Nitric Oxide Pathway Dysregulation in Fabry Disease (2001)

These findings suggest a chronic alteration of the nitric oxide pathway in Fabry disease, with critical protein nitration that is reversible with enzyme replacement therapy.
Concurrent learning adaptive control of linear systems with exponentially convergent bounds (2012)

SUMMARY Concurrent learning adaptive controllers, which use recorded and current data concurrently for adaptation, are developed for model reference adaptive control of uncertain linear dynamical systems. We show that a verifiable condition on the linear independence of the recorded data is sufficient to guarantee global exponential stability. We use this fact to develop exponentially decaying bounds on the tracking error and weight error, and estimate upper bounds on the control signal. These results allow the development of adaptive controllers that ensure good tracking without relying on high adaptation gains, and can be designed to avoid actuator saturation. Simulations and hardware experiments show improved performance. Copyright © 2012 John Wiley &amp; Sons, Ltd.
Chronic Stress Induces Contrasting Patterns of Dendritic Remodeling in Hippocampal and Amygdaloid Neurons (2002)

The hippocampus and the amygdala are essential components of the neural circuitry mediating stress responses. The hippocampus, which provides negative feedback regulation of the stress response, is particularly vulnerable to degenerative changes caused by chronic stress. Unlike the hippocampus, relatively little is known about how stress affects the amygdala and the nature of its role in the stress response. Hence, we examined the effects of two different models of chronic stress on hippocampal and amygdaloid neuronal morphology in rats. In agreement with previous reports, chronic immobilization stress (CIS) induced dendritic atrophy and debranching in CA3 pyramidal neurons of the hippocampus. In striking contrast, pyramidal and stellate neurons in the basolateral complex of the amygdala exhibited enhanced dendritic arborization in response to the same CIS. Chronic unpredictable stress (CUS), however, had little effect on CA3 pyramidal neurons and induced atrophy only in BLA bipolar neurons. These results indicate that chronic stress can cause contrasting patterns of dendritic remodeling in neurons of the amygdala and hippocampus. Moreover, CIS, but not CUS, reduced open-arm activity in the elevated plus-maze. These findings raise the possibility that certain forms of chronic stress, by affecting specific neuronal elements in the amygdala, may lead to behavioral manifestations of enhanced emotionality. Thus, stress-induced structural plasticity in amygdala neurons may provide a candidate cellular substrate for affective disorders triggered by chronic stress.
Photoinduced Ligand-to-Metal Charge Transfer Enables Photocatalyst-Independent Light-Gated Activation of Co(II) (2018)

Photoredox catalysis can be used to manipulate the redox state of a transition metal complex leading to the desired reactivity. While powerful, obviating the role of the second catalyst would be attractive from the perspective of simplifying the protocol and using visible light to uncover unexpected, enabling reactivity. Herein we report that Co-acetylides, formed in situ, are photoactive complexes that undergo ligand-to-metal charge transfer using visible light. The net transformation uses air-stable Co(II) complexes as precatalysts and induces Co(I) chemistry. The acetylide is an electron reservoir forming the Co(I) but accepting the electron back at the end of the catalytic cycle. The electronic nature of the acetylide leads to either on–off behavior or simply initiates catalysis, depending on electronics.
Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases (2002)

We have searched for sulfate-reducing bacteria in the feces of 41 healthy individuals and 110 patients from a Hepato-Gastro-Enterology Unit using a specific liquid medium (Test-kit Labège, Compagnie Française de Géothermie, Orléans, France). The 110 patients were separated in 22 patients presenting with inflammatory bowel diseases and 88 patients hospitalized for other lower (n=30) or upper (n=58) digestive tract diseases. Sulfate-reducing bacteria were isolated from 10 healthy individuals (24%), 15 patients presenting with inflammatory bowel diseases (68%), and 33 patients with other symptoms (37%). A multiplex PCR was devised for the identification of Desulfovibrio piger (formerly Desulfomonas pigra), Desulfovibrio fairfieldensis and Desulfovibrio desulfuricans, and applied to the above isolates. The strains of sulfate-reducing bacteria consisted of D. piger (39 isolates), D. fairfieldensis (19 isolates) and D. desulfuricans (one isolate). The prevalence of D. piger was significantly higher in inflammatory bowel disease patients (55%) as compared to healthy individuals (12%) or patients with other symptoms (25%) (P<0.05).
Design of a multi-media vehicle for social browsing (1988)

In this paper we present a new approach to the use of computer-mediated communications technology to support distributed cooperative work. In contrast to most of the existing approaches to CSCW, we focus explicitly on tools to enable unplanned, informal social interaction. We describe a “social interface” which provides direct, low-cost access to other people through the use of multi-media communications channels. The design of the system centers around three basic concepts derived from the research literature and our own observations of the workplace: social browsing, a virtual workplace, and interaction protocols. We use these design properties to describe a new system concept, and examine the implications for CSCW of having automated social interaction available through the desktop workstation.
Designing for collaborative creative problem solving (2007)

Collaborative creativity is traditionally supported by formal techniques, such as brainstorming. These techniques improve the idea-generation process by creating group synergies, but also suffer from a number of negative effects. Current electronic tools to support collaborative creativity overcome some of these problems, but introduce new ones, by either losing the benefits of face-to-face communication or the immediacy of simultaneous contribution. Using an interactive environment as a test bed, we are investigating how collaborative creativity can be supported electronically while maintaining face-to-face communication. What are the design-factors influencing such a system? We have designed a brainstorming application that uses an interactive table and a large wall display, and compared the results of using it to traditional paper-based brainstorming in a user study with 30 participants. From the considerations that went into the design and the observations during the study we derive a number of design guidelines for collaborative systems in interactive environments.
Biomimetic macroporous hydrogel scaffolds in a high‐throughput screening format for cell‐based assays (2008)

Macroporous hydrogels (MHs) hold great promise as scaffolds in tissue engineering and cell-based assays. In this study, the possibility of combination of three-dimensional (3D) cell culture with a miniaturized screening format was demonstrated on human colon cancer HCT116, human acute myeloid leukemia KG-1 cells, and embryonic fibroblasts cultured on MHs (12.5 mm x 7.1 mm I.D.) in a 96-minicolumn plate format. MHs were prepared by cryogelation technique and functionalized by coating with type I collagen and by copolymerization with agmatine-based mimetic of cell adhesive peptide RGD (abRGDm). Cancer cells formed multicellular aggregates while fibroblasts formed adhesions on abRGDm-containing and collagen-MHs but not on plain MHs, as was demonstrated by scanning electron microscopy. HCT116 and KG-1 cells grown as aggregates were more resistant to the treatment with cis-diaminedichloroplatinum (II) (cisplatin) and cytosine 1-beta-D-arabinofuranoside (Ara-C), respectively, during the first 18-24 h of incubation, than single cells grown on unmodified MH. HCT116 cells grown as 2D cultures in conventional 96-well tissue culture plates were 1.5- to 3.5-fold more sensitive to the treatment with 70 microM cisplatin than cells in 3D cultures in functionalized MHs. Further development of the described experimental system including matching of a specific cell type with appropriate extracellular matrix (ECM) components and 3D cocultures on ECM-modified MHs may provide a realistic in vitro experimental model for high-throughput toxicity tests.
The Public Health Impact of Alzheimer's Disease, 2000–2050: Potential Implication of Treatment Advances (2002)

Recent developments in basic research suggest that therapeutic breakthroughs may occur in Alzheimer's disease treatment over the coming decades. To model the potential magnitude and nature of the effect of these advances, historical data from congestive heart failure and Parkinson's disease were used. Projections indicate that therapies which delay disease onset will markedly reduce overall disease prevalence, whereas therapies to treat existing disease will alter the proportion of cases that are mild as opposed to moderate/severe. The public health impact of such changes would likely involve both the amount and type of health services needed. Particularly likely to arise are new forms of outpatient services, such as disease-specific clinics and centers. None of our models predicts less than a threefold rise in the total number of persons with Alzheimer's disease between 2000 and 2050. Therefore, Alzheimer's care is likely to remain a major public health problem during the coming decades.