gebhart/patrepeval huggingface dataset:
Anticipatory Suppression of Nonattended Locations in Visual Cortex Marks Target Location and Predicts Perception (2008)

Spatial attention is associated with modulations in prestimulus, anticipatory blood oxygen level-dependent (BOLD) activity across the brain. It is unclear, however, if these anticipatory modulations depend on the computational demands of the upcoming task. Here, we show that anticipation of low-contrast stimuli, relative to high-contrast stimuli, is associated with increased prestimulus BOLD activity in the frontal eye field (FEF) and the posterior inferior frontal sulcus (IFS) but not in the intraparietal sulcus (IPS). In visual cortex, anticipation of low-contrast stimuli is associated with increased suppression of activity corresponding to unattended (but not attended) locations, and this suppression predicts whether subjects will accurately perceive low-contrast stimuli. These results suggest that when a stimulus will be difficult to distinguish from the background, top-down signals from FEF and IFS can facilitate perception by marking its location through the suppression of unattended locations in visual cortex.
Why phishing works (2006)

To build systems shielding users from fraudulent (or phishing) websites, designers need to know which attack strategies work and why. This paper provides the first empirical evidence about which malicious strategies are successful at deceiving general users. We first analyzed a large set of captured phishing attacks and developed a set of hypotheses about why these strategies might work. We then assessed these hypotheses with a usability study in which 22 participants were shown 20 web sites and asked to determine which ones were fraudulent. We found that 23% of the participants did not look at browser-based cues such as the address bar, status bar and the security indicators, leading to incorrect choices 40% of the time. We also found that some visual deception attacks can fool even the most sophisticated users. These results illustrate that standard security indicators are not effective for a substantial fraction of users, and suggest that alternative approaches are needed.
Monoclonal Antibodies Defining Distinctive Human T Cell Surface Antigens (1979)

Three novel nonoclonal antibodies (designed OKT1, OKT3, and OKT4) were generated against surface determinants of human peripheral T cells. Both OKT1 and OKT3 reacted with all human peripheral T cells and 5 to 10 percent of thymocytes but differed in their reactivities with T cel- lines. By contrast, OKT4 reacted with 55 percent of human peripheral T cells and 80 percent of thymocyted in that they did not react with normal B cells, null cells, monocytes, or granulocytes.
Development of mice expressing a single D-type cyclin (2002)

D-cyclins (cyclins D1, D2, and D3) are components of the core cell cycle machinery. To directly test the ability of each D-cyclin to drive development of various lineages, we generated mice expressing only cyclin D1, or only cyclin D2, or only cyclin D3. We found that these "single-cyclin" embryos develop normally until late gestation. Our analyses revealed that in single-cyclin embryos, the tissue-specific expression pattern of D-cyclins was lost. Instead, mutant embryos ubiquitously expressed the remaining D-cyclin. These findings suggest that the functions of the three D-cyclins are largely exchangeable at this stage. Later in life, single-cyclin mice displayed focused abnormalities, resulting in premature mortality. "Cyclin D1-only" mice developed severe megaloblastic anemia, "cyclin D2-only" mice presented neurological abnormalities, and "cyclin D3-only" mice lacked normal cerebella. Analyses of the affected tissues revealed that these compartments failed to sufficiently up-regulate the remaining, intact D-cyclin. In particular, we found that in cerebellar granule neuron precursors, the N-myc transcription factor communicates with the cell cycle machinery via cyclins D1 and D2, but not D3, explaining the inability of D3-only mice to up-regulate cyclin D3 in this compartment. Hence, the requirement for a particular cyclin in a given tissue is likely caused by specific transcription factors, rather than by unique properties of cyclins.
Presence of Fetal RNA in Maternal Plasma (2000)

The discovery of fetal DNA in maternal plasma (1) has opened up a new horizon on prenatal molecular diagnosis. Many groups have since shown that fetal genetic traits, such as RhD status and inherited genetic diseases, can be determined from fetal DNA in maternal plasma (2)(3)(4)(5). However, it is not known whether fetal RNA is also present in maternal plasma. Here, using a two-step reverse transcription (RT)-PCR assay, we demonstrate the presence of fetal-derived, male-specific mRNA in plasma of pregnant women carrying male fetuses.

Pregnant women attending the Prenatal Diagnosis Unit at the Department of Obstetrics and Gynecology, Prince of Wales Hospital, Hong Kong were recruited with informed consent. The study was approved by the Clinical Research Ethics Committee. Women early and late in their pregnancies (n = 21 and 37, respectively) were recruited in this study. The mean gestational ages of the subjects in early and late pregnancies were 16 weeks (range, 11–19 weeks) and 33 weeks (range, 26–40 weeks), respectively. All early-pregnancy samples were obtained before any invasive procedure. On the other hand, late-pregnancy samples were collected either from women who had invasive procedures in early pregnancy (n = 21) or from women who did not have any prenatal invasive procedure (n = 16). All plasma samples were harvested within 30 min from EDTA-blood samples as described previously (1). Total RNA from plasma samples was isolated with the Trizol LS Reagent (Life Technologies) as instructed …
Pseudomonas pseudoalcaligenes subsp. konjaci subsp. nov., the Causal Agent of Bacterial Leaf Blight of Konjac (Amorphophalus konjac Koch.) (1983)

A bacterial disease characterized by the development of rectangular lesions on the leaves of konjac (Amorphophalus konjac Koch.) is described. The size of the lesions increased rapidly under humid conditions, resulting in leaf blight. Leaves with severe blight drooped and finally decayed. The disease was identified from the symptoms as bacterial leaf blight on the basis of the descriptions made by Uyeda in 1910. The causal agent was, however, different from Xanthomonas conjaci (Uyeda) Burkholder in many respects and was found to be a new subspecies of Pseudomonas pseudoalcaligenes based on the results of a direct comparison of pathological and biochemical properties. The name Pseudomonas pseudoalcaligenes subsp. konjaci subsp. nov. is proposed for the new subspecies, and strain K2 (= ATCC 33996 = PDDCC 7733) is designated the type strain.
CRISPR-mediated TCR replacement generates superior anticancer transgenic T cells (2017)

Adoptive transfer of T cells genetically modified to express a cancer-specific T-cell receptor (TCR) has shown significant therapeutic potential for both hematological and solid tumors. However, a major issue of transducing T cells with a transgenic TCR is the preexisting expression of TCRs in the recipient cells. These endogenous TCRs compete with the transgenic TCR for surface expression and allow mixed dimer formation. Mixed dimers, formed by mispairing between the endogenous and transgenic TCRs, may harbor autoreactive specificities. To circumvent these problems, we designed a system where the endogenous TCR-β is knocked out from the recipient cells using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein-9 (Cas9) technology, simultaneously with transduction with a cancer-reactive receptor of choice. This TCR replacement strategy resulted in markedly increased surface expression of transgenic αβ and γδ TCRs, which in turn translated to a stronger, and more polyfunctional, response of engineered T cells to their target cancer cell lines. Additionally, the TCR-plus-CRISPR-modified T cells were up to a thousandfold more sensitive to antigen than standard TCR-transduced T cells or conventional model proxy systems used for studying TCR activity. Finally, transduction with a pan-cancer-reactive γδ TCR used in conjunction with CRISPR/Cas9 knockout of the endogenous αβ TCR resulted in more efficient redirection of CD4<sup>+</sup> and CD8<sup>+</sup> T cells against a panel of established blood cancers and primary, patient-derived B-cell acute lymphoblastic leukemia blasts compared with standard TCR transfer. Our results suggest that TCR transfer combined with genome editing could lead to new, improved generations of cancer immunotherapies.
Inertial Focusing in Microfluidics (2014)

When Segré and Silberberg in 1961 witnessed particles in a laminar pipe flow congregating at an annulus in the pipe, scientists were perplexed and spent decades learning why such behavior occurred, finally understanding that it was caused by previously unknown forces on particles in an inertial flow. The advent of microfluidics opened a new realm of possibilities for inertial focusing in the processing of biological fluids and cellular suspensions and created a field that is now rapidly expanding. Over the past five years, inertial focusing has enabled high-throughput, simple, and precise manipulation of bodily fluids for a myriad of applications in point-of-care and clinical diagnostics. This review describes the theoretical developments that have made the field of inertial focusing what it is today and presents the key applications that will make inertial focusing a mainstream technology in the future.
Gamma-crystallins of the human eye lens: expression analysis of five members of the gene family. (1987)

While only two gamma-crystallins have been identified in the human eye lens, molecular studies indicate that the human gamma-crystallins are encoded in a multigene family comprising at least seven closely related members. Sequence analysis of five of these genes has suggested that three (gamma 1-2, G3, and G4) are potentially active, while two (G1 psi and G2 psi) correspond to closely related pseudogenes. Here we report on the detailed structure of a sixth gamma-crystallin gene, G5, and our results obtained with transient expression assays to characterize both the promoter activity and translation products of five members of the gene family. We show that 5'-flanking sequences of G1 psi and G2 psi lacked detectable promoter activity, while the corresponding sequences of G3, G4, and G5 were able to direct high levels of expression of the bacterial chloramphenicol acetyltransferase gene in primary lens epithelia, but not in cultures of nonlens origin. Detailed sequence comparisons indicated that active genes contained several conserved sequence tracts 5' of the TATA box which may constitute functional elements of a lens-specific gamma-crystallin promoter. Expression of the gamma-crystallin coding sequences from the human metallothionein IIA promoter in nonlens cells facilitated characterization of the polypeptides encoded by individual gamma-genes and, in future studies, should permit comparison of these proteins with distinct gamma-crystallins in the human lens.
Improved allelic exchange vectors and their use to analyze 987P fimbria gene expression (1998)

A series of vectors has been developed to provide improved positive and negative selection for allelic exchange. Based on homologous regions of DNA ranging in size from less than 200 bp to over 1 kb, we have successfully used these new plasmids to introduce or remove markers in chromosomal or plasmid DNA. Wild type fimbria genes were replaced both in Salmonella enteritidis (sefA, agfA and fimC) and Escherichia coli (fasA and fasH). Regulation of 987P fimbriation could be identified after replacement of fasA and fasH with allelic reporter fusions. The expression of fasA but not fasH is dependent upon the osmolarity of the growth medium in an HNS-dependent manner, but unlike some other fimbrial systems expression is not dependent on the exogenous iron concentration.
Hallmarks of Cancer: The Next Generation (2011)

The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors. The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease. They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis. Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions. Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list-reprogramming of energy metabolism and evading immune destruction. In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the "tumor microenvironment." Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer.
Neural Voice Cloning with a Few Samples (2018)

Voice cloning is a highly desired feature for personalized speech interfaces. Neural network based speech synthesis has been shown to generate high quality speech for a large number of speakers. In this paper, we introduce a neural voice cloning system that takes a few audio samples as input. We study two approaches: speaker adaptation and speaker encoding. Speaker adaptation is based on fine-tuning a multi-speaker generative model with a few cloning samples. Speaker encoding is based on training a separate model to directly infer a new speaker embedding from cloning audios and to be used with a multi-speaker generative model. In terms of naturalness of the speech and its similarity to original speaker, both approaches can achieve good performance, even with very few cloning audios. While speaker adaptation can achieve better naturalness and similarity, the cloning time or required memory for the speaker encoding approach is significantly less, making it favorable for low-resource deployment.
Differential recognition of a protective filarial antigen by antibodies from humans with bancroftian filariasis. (1986)

The objectives of this study were to identify filarial antigens which induce enhanced clearance of circulating microfilariae and to establish if human antibody reactivity with these molecules correlates with the apparent parasite burdens of residents of an endemic area of Bancroftian filariasis. Mice immunized with an extract of Brugia malayi microfilariae develop IgG antibodies to four major filarial antigens with an apparent molecular weight (Mr) of approximately 112,000, 60,000, 45,000, and 25,000. Animals immunized with gel slices containing the approximately 25,000-Mr antigen are resistant to intravenous challenge with live microfilariae (78-98% reduction in parasitemia vs. controls, P less than 0.01). A group of 22 amicrofilaremic humans had a significantly higher (P less than 0.025) mean antibody titer to the Mr 25,000-Mr antigen (1: 424) than 16 microfilaremic individuals (1:95). There were no significant differences between the two groups in antibody titers to filarial antigens of Mr approximately 112,000, 60,000, and 45,000 Mr. These data suggest that a high degree of reactivity to the 25,000-Mr antigen in humans with lymphatic filariasis correlates with a parasitologic status that is least conducive to transmission of infection.
Privacy-Preserving Set Operations (2005)

In many important applications, a collection of mutually distrustful parties must perform private computation over multisets.Each party's input to the function is his private input multiset.In order to protect these private sets, the players perform privacy-preserving computation; that is, no party learns more information about other parties' private input sets than what can be deduced from the result.In this paper, we propose efficient techniques for privacy-preserving operations on multisets.By employing the mathematical properties of polynomials, we build a framework of efficient, secure, and composable multiset operations: the union, intersection, and element reduction operations.We apply these techniques to a wide range of practical problems, achieving more efficient results than those of previous work.
Overexpression of Full-Length ETV1 Transcripts in Clinical Prostate Cancer Due to Gene Translocation (2011)

ETV1 is overexpressed in a subset of clinical prostate cancers as a fusion transcript with many different partners. However, ETV1 can also be overexpressed as a full-length transcript. Full-length ETV1 protein functions differently from truncated ETV1 produced by fusion genes. In this study we describe the genetic background of full-length ETV1 overexpression and the biological properties of different full-length ETV1 isoforms in prostate cancer. Break-apart FISH showed in five out of six patient samples with overexpression of full-length ETV1 a genomic rearrangement of the gene, indicating frequent translocation. We were able to study the rearrangements in more detail in two tumors. In the first tumor 5'-RACE on cDNA showed linkage of the complete ETV1 transcript to the first exon of a prostate-specific two exon ncRNA gene that maps on chromosome 14 (EST14). This resulted in the expression of both full-length ETV1 transcripts and EST14-ETV1 fusion transcripts. In chromosome spreads of a xenograft derived from the second prostate cancer we observed a complex ETV1 translocation involving a chromosome 7 fragment that harbors ETV1 and fragments of chromosomes 4 and 10. Further studies revealed the overexpression of several different full-length transcripts, giving rise to four protein isoforms with different N-terminal regions. Even the shortest isoform synthesized by full-length ETV1 stimulated in vitro anchorage-independent growth of PNT2C2 prostate cells. This contrasts the lack of activity of even shorter N-truncated ETV1 produced by fusion transcripts. Our findings that in clinical prostate cancer overexpression of full-length ETV1 is due to genomic rearrangements involving different chromosomes and the identification of a shortened biologically active ETV1 isoform are highly relevant for understanding the mechanism of ETV1 function in prostate cancer.
Self-Assembly of Nanoparticles in Three-Dimensions:  Formation of Stalagmites (2005)

We develop a coarse-grained lattice gas model to describe drying-mediated self-assembly of nanoparticles in three dimensions. Our model is an extension of the model developed by Rabani et al. [Nature 2003, 426, 271] in two dimensions. We show that when liquid evaporation occurs layer by layer and solvation forces are strong, the resulting morphologies agree well with the predictions of the 2D model. We discuss scenarios in which the full 3D treatment is necessary and predict the formation of nanostalagmites.
A categoria da existência na refutação kantiana do argumento ontológico (2023)

Resumo
Specificity of rabies virus as a transneuronal tracer of motor networks: Transfer from hypoglossal motoneurons to connected second‐order and higher order central nervous system cell groups (1995)

The specificity of transneuronal transfer of rabies virus [challenge virus standard (CVS) strain] was evaluated in a well-characterized neuronal network, i.e., retrograde infection of hypoglossal motoneurons and transneuronal transfer to connected (second-order) brainstem neurons. The distribution of the virus in the central nervous system was studied immunohistochemically at sequential intervals after unilateral inoculation into the hypoglossal nerve. The extent of transneuronal transfer of rabies virus was strictly time dependent and was distinguished in five stages. At 1 day postinoculation, labelling involved only hypoglossal motoneurons (stage 1). Retrograde transneuronal transfer occurred from 2.0-2.5 days postinoculation (stage 2). In stages 2-4, different groups of second-order neurons were labelled sequentially, depending on the strength of their input to the hypoglossal nucleus. In stages 4 and 5, labelling extended to several cortical and subcortical cell groups, which can be regarded as higher order because they are known to control tongue movements and/or to provide input to hypoglossal-projecting cell groups. The pattern of transneuronal transfer of rabies virus resembles that of alpha-herpesviruses with regard to the nonsynchronous labelling of different groups of second-order neurons and the transfer to higher order neurons. In striking contrast to alpha-herpesviruses, the transneuronal transfer of rabies is not accompanied by neuronal degeneration. Moreover, local spread of rabies from infected neurons and axons to adjoining glial cells, neurons, or fibers of passage does not occur. The results show that rabies virus is a very efficient transneuronal tracer. Results also provide a new insight into the organization of cortical and subcortical higher order neurons that mediate descending control of tongue movements indirectly via hypoglossal-projecting neurons.
Fluorescence detection of tumors early diagnosis of microscopic lesions in preclinical studies (1993)

With the use of the hamster buccal cavity model involving the initiation and promotion of premalignant and malignant conditions by 9,10 dimethyl-1,2-benzanthracene, the technique could discern these two stages of disease with significance levels that were less than 0.05 and 0.01, respectively.
A Network Based On Inter-vehicle Communication (2005)

This paper presents an inter-vehicle networking method as a means of data exchange. By using this method, each vehicle can know the position of its neighboring vehicles, the traffic information captured by other vehicles, and the neighbor node's information such as speed or braking. Spread Spectrum communications, using optical media, is used to create links for the data transmission.
Hambone: A Bio-Acoustic Gesture Interface (2007)

Mobile input technologies can be bulky, obtrusive, or difficult to use while performing other tasks. In this paper, we present Hambone, a lightweight, unobtrusive system that affords quick access, subtlety, and multitasking capabilities for gesture-based mobile device interaction. Hambone uses two small piezoelectric sensors placed on either the wrist or ankle. When a user moves his hands or feet, the sounds generated by the movement travel to Hambone via bone conduction. Hambone then transmits the signals digitally to a mobile device or computer. The signals are recognized using hidden Markov models (HMMs) and are mapped to a set of commands controlling an application. In this paper, we present the hardware and software implementation of Hambone, a preliminary evaluation, and a discussion of future opportunities in bio-acoustic gesture-based interfaces.