gebhart/patrepeval huggingface dataset:
A CMOS area image sensor with pixel-level A/D conversion (2002)

Charge-coupled devices (CCD) are at present the most widely used technology for implementing area image sensors. However, they suffer from low yields, consume too much power, and are plagued with SNR limitations due to the shifting and detection of analog charge packets, and the fact that data is communicated off chip in analog form. This paper describes an area image sensor that can potentially circumvent the limitations of CCDs and their alternatives. It uses a standard CMOS process and can therefore be manufactured with high yield. Digital circuitry for control and signal processing can be integrated with the sensor. Moreover, CMOS technology advances such as scaling and extra layers of metal can be used to improve pixel density and sensor performance. The analog image data is immediately converted to digital at each pixel using a one-bit sigma-delta modulator. The use of sigma-delta modulation allows the data-conversion circuitry to be simple and insensitive to process variations. A global shutter provides variable light input attenuation to achieve wide dynamic range. Data is communicated off chip in a digital form, eliminating the SNR degradation of analog data communication. To demonstrate the viability of the approach, an area image sensor chip is fabricated in a 1.2 /spl mu/m CMOS technology. The device consists of an array of 64x64 pixel blocks, a clock driver, a 6:64 row address decoder, 64 latched sense amplifiers, and 16 4:1 column multiplexers. The chip also contains data compression circuitry.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
PhLPs and PhLOPs in the Phosducin Family of Gβγ Binding Proteins (1998)

In this study, we identify new isoforms of the retinal phosducin and investigate the expression of the phosducin family, showing that an isoform, PhLP1, has sequence homology with Phd and Gbeta gamma binding capability, whereas two isoforms (phosducin-like orphan proteins, PhLOPs) share sequence homology with Phd but fail to bind Gbeta gamma. Original identification of PhLP1 and the PhLOPs was from a human retina cDNA library, using a PCR product for library hybridization screening that contained a predicted functional epitope domain. The screen identified Phd and three related, but distinct, recombinants (PhLP1, PhLOP1, and PhLOP2). By RT-PCR, all isoforms are expressed in either retina or forskolin-stimulated Y79 retinoblastoma cells; however, the new isoforms are below the level of detection on Northern blot analysis. The predicted amino acid translation of each homologue revealed major differences, arising from either splice variants or gene duplication of Phd. To test the functional interaction of all phosducin isoforms with Gbeta gamma in vitro, a glutathione S-transferase (GST) fusion protein was developed for each member. Biochemical interaction with purified retinal transducin Gbeta gamma was verified for GST-Phd and demonstrated for GST-PhLP1; however, neither GST-PhLOP1 nor GST-PhLOP2 bound Gbeta gamma. Comparable results were observed when the GST-phosducin fusion proteins selectively sequestered Gbeta gammas from retinal extracts or when functional Gbeta gamma interactions were assessed using surface plasmon resonance technology. Phosducin and its isoforms are widely distributed in body tissues where they may participate in signal transduction pathways. Phd and PhLP1 possess an 11-amino acid conserved epitope domain (TGPKGVINDWR) that controls the high-affinity binding of Gbeta gamma; these isoforms are implicated in the G-protein signaling pathway. The phosducin-like orphan proteins (PhLOPs) fail to bind Gbeta gamma, suggesting that the PhLOP isoforms may participate in still unidentified signaling pathways.
BranchScope (2018)

We present BranchScope - a new side-channel attack where the attacker infers the direction of an arbitrary conditional branch instruction in a victim program by manipulating the shared directional branch predictor. The directional component of the branch predictor stores the prediction on a given branch (taken or not-taken) and is a different component from the branch target buffer (BTB) attacked by previous work. BranchScope is the first fine-grained attack on the directional branch predictor, expanding our understanding of the side channel vulnerability of the branch prediction unit. Our attack targets complex hybrid branch predictors with unknown organization. We demonstrate how an attacker can force these predictors to switch to a simple 1-level mode to simplify the direction recovery. We carry out BranchScope on several recent Intel CPUs and also demonstrate the attack against an SGX enclave.
Tauroursodeoxycholic acid reduces apoptosis and protects against neurological injury after acute hemorrhagic stroke in rats (2003)

Tauroursodeoxycholic acid (TUDCA), an endogenous bile acid, modulates cell death by interrupting classic pathways of apoptosis. Intracerebral hemorrhage (ICH) is a devastating acute neurological disorder, without effective treatment, in which a significant loss of neuronal cells is thought to occur by apoptosis. In this study, we evaluated whether TUDCA can reduce brain injury and improve neurological function after ICH in rats. Administration of TUDCA before or up to 6 h after stereotaxic collagenase injection into the striatum reduced lesion volumes at 2 days by as much as 50%. Apoptosis was approximately 50% decreased in the area immediately surrounding the hematoma and was associated with a similar inhibition of caspase activity. These changes were also associated with improved neurobehavioral deficits as assessed by rotational asymmetry, limb placement, and stepping ability. Furthermore, TUDCA treatment modulated expression of certain Bcl-2 family members, as well as NF-kappaB activity. In addition to its protective action at the mitochondrial membrane, TUDCA also activated the Akt-1protein kinase Balpha survival pathway and induced Bad phosphorylation at Ser-136. In conclusion, reduction of brain injury underlies the wide-range neuroprotective effects of TUDCA after ICH. Thus, given its clinical safety, TUDCA may provide a potentially useful treatment in patients with hemorrhagic stroke and perhaps other acute brain injuries associated with cell death by apoptosis.
Effects of electron-boundary scattering on changes in thermoreflectance in thin metal films undergoing intraband excitations (2009)

As characteristic sizes and lengths scales continue to decrease in nanostructures, carrier scattering processes at the geometric boundaries and interfaces in nanosystems become more prevalent. These scattering events can lead to additional resistances. This paper investigates electron-boundary scattering processes by examining changes in thermoreflectance signals in thin films after short pulsed laser heating. To take electron-boundary scattering into account, an additional scattering term is introduced into the Drude model for the complex dielectric function. Using an intraband thickness-dependent reflectance model, transient thermoreflectance data of Au films subject to intraband excitations are analyzed with the electron-boundary scattering Drude model introduced in this work. The electron-boundary scattering rate is determined from Au thermoreflectance data, showing that after short pulsed laser heating, electron-boundary scattering rates can be almost three orders of magnitude greater than the electron-electron and electron-phonon scattering rates. The scattering rates determined from the thermoreflectance data agree well with the theoretical predictions for electron-boundary scattering calculated from an electron-boundary scattering model for disordered conductors in the event of an electron-phonon nonequilibrium.
Chemical Approaches to Control Gene Expression (2001)

A current goal in molecular medicine is the development of new strategies to interfere with gene expression in living cells in the hope that novel therapies for human disease will result from these efforts. This review focuses on small-molecule or chemical approaches to manipulate gene expression by modulating either transcription of messenger RNA-coding genes or protein translation. The molecules under study include natural products, designed ligands, and compounds identified through functional screens of combinatorial libraries. The cellular targets for these molecules include DNA, messenger RNA, and the protein components of the transcription, RNA processing, and translational machinery. Studies with model systems have shown promise in the inhibition of both cellular and viral gene transcription and mRNA utilization. Moreover, strategies for both repression and activation of gene transcription have been described. These studies offer promise for treatment of diseases of pathogenic (viral, bacterial, etc.) and cellular origin (cancer, genetic diseases, etc.).
Improvement of the MALDI-TOF Analysis of DNA with Thin-Layer Matrix Preparation (2002)

A new method of sample preparation was developed for MALDI-TOF-MS analysis of oligonucleotides. First, aqueous DNA samples are dispensed and allowed to dry. Then 6-aza-2-thiothymine matrix dissolved in nonaqueous volatile solvents is applied on top of the DNA residue to form a thin homogeneous film. MALDI-TOF analysis shows such preparation generates much better shot-to-shot and sample-to-sample reproducibility and essentially eliminates the need to search for "hot" spots. The increased homogeneity of the matrix/analyte crystal distribution results in significant improvement for quantitative and high-throughput analyses of DNA. Using this method, isotopically resolved oligonucleotide spectra up to a 24-mer can also be easily obtained in a reflectron instrument. Due to the ease of preparation, this method could be widely useful for a number of applications such as for assays that are performed on surface in vitro, as the thin-layer matrix could be applied directly for MALDI analysis.
Restenosis (1993)

Division of Cardiovascular Diseases and Internal Medicine, Mayo Clinic and Mayo Foundation, Rochester, MN, USA.
HIV Superinfection (2005)

Worldwide, 16 cases of HIV-1 superinfection in humans have been reported since 2002. Superinfection is defined as the reinfection of an individual who already has an established infection with a heterologous HIV strain. Controversy exists surrounding superinfection, because it has implications concerning our understanding of worldwide HIV diversity, individual immunity and disease progression, and vaccine development. Here, we review the current understanding of HIV superinfection.
Face spoofing detection through partial least squares and low-level descriptors (2011)

Personal identity verification based on biometrics has received increasing attention since it allows reliable authentication through intrinsic characteristics, such as face, voice, iris, fingerprint, and gait. Particularly, face recognition techniques have been used in a number of applications, such as security surveillance, access control, crime solving, law enforcement, among others. To strengthen the results of verification, biometric systems must be robust against spoofing attempts with photographs or videos, which are two common ways of bypassing a face recognition system. In this paper, we describe an anti-spoofing solution based on a set of low-level feature descriptors capable of distinguishing between 'live' and 'spoof images and videos. The proposed method explores both spatial and temporal information to learn distinctive characteristics between the two classes. Experiments conducted to validate our solution with datasets containing images and videos show results comparable to state-of-the-art approaches.
Christchurch Psychiatric Epidemiology Study, Part I: Methodology and Lifetime Prevalence for Specific Psychiatric Disorders (1989)

In 1986 the Christchurch Psychiatric Epidemiology Study obtained interviews with a probability sample of 1498 adults aged 18 to 64 years. The Diagnostic Interview Schedule (DIS) was used to enable DSM-III diagnoses to be made. This paper describes the methodology of the study and reports the lifetime prevalence of specific psychiatric disorders. The highest lifetime prevalences found were for generalised anxiety (31%), alcohol abuse/dependence (19%) and major depressive episode (13%). Men had higher rates of substance abuse whereas women had higher rates of affective disorders and most anxiety disorders. Compared with results from the Epidemiologic Catchment Area Program, Puerto Rico and Edmonton, Christchurch has the highest rates for major depression and is among the highest for alcohol abuse/dependence.
Acute neuropathology in soman poisoned rats. (1984)

Groups of rats received single subcutaneous injections of the highly toxic organophosphate compound, soman, in doses of 106, 133 or 165 micrograms/kg and were observed during the acute phase of intoxication. Survivors were killed at intervals up to fourteen days after exposure, and brain sections were examined by light microscopy. A consistent pattern of neuronal degeneration and necrosis was observed in brains of animals which had experienced convulsions during the intoxication. The lesions had an appearance and distribution similar to that reported for both hypoxic injury and status epilepticus. No lesions were observed in animals which did not experience convulsions. The results indicate that soman, and possibly other similar organophosphate compounds, may produce significant irreversible damage to the central nervous system.
Influence of growth rate on susceptibility to antimicrobial agents: biofilms, cell cycle, dormancy, and stringent response (1990)

Article de synthese portant sur les facteurs influancant la sensibilite resistance des microorganismes aux antimicrobiens.
Lowt3 syndrome with asynchronous changes of tt3 and rt3 values in laparoscopic cholecystectomy (1998)

Non-thyroidal illnesses, such as surgical stress, are associated with abnormal metabolism of thyroid hormones. However, the potential impact of variable surgical procedures remain to be elucidated. In order to evaluate the effect of mild surgical stress upon thyroid function, TT4, TT3, rT3 and TSH were measured in twenty-two patients undergoing laparoscopic cholecystectomy before (Stage 1), during (Stages 2-5), at the recovery room (Stage 6) and 24h postoperatively (Stage 7). The values of TSH remained within the normal limits with transient changes during the study period. Similarly, TT4 values displayed normal variations within the normal range without reaching a statistically significant difference during the study period. A decrease of TT3 values was detected early at stage 2 during induction of anaesthesia. TT3 remained at low levels during the perioperative period, and a further decrease was observed 24 h postoperatively. The above profile of thyroid hormone metabolism, reflects a low-T3 syndrome in patients undergoing laparoscopic cholecystectomy. Interestingly, there was a tendency for rT3 to increase and it reach its highest value 24h postoperatively with the difference being statistically significant (p<0.05). The asynchronous distribution of rT3 and TT3 might be attributed to multifactorial influences.
Short‐chain dehydrogenases/reductases (SDRs) (2002)

Short-chain dehydrogenases/reductases (SDRs) are enzymes of great functional diversity. Even at sequence identities of typically only 15-30%, specific sequence motifs are detectable, reflecting common folding patterns. We have developed a functional assignment scheme based on these motifs and we find five families. Two of these families were known previously and are called 'classical' and 'extended' families, but they are now distinguished at a further level based on coenzyme specificities. This analysis gives seven subfamilies of classical SDRs and three subfamilies of extended SDRs. We find that NADP(H) is the preferred coenzyme among most classical SDRs, while NAD(H) is that preferred among most extended SDRs. Three families are novel entities, denoted 'intermediate', 'divergent' and 'complex', encompassing short-chain alcohol dehydrogenases, enoyl reductases and multifunctional enzymes, respectively. The assignment scheme was applied to the genomes of human, mouse, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae. In the animal genomes, the extended SDRs amount to around one quarter or less of the total number of SDRs, while in the A. thaliana and S. cerevisiae genomes, the extended members constitute about 40% of the SDR forms. The numbers of NAD(H)-dependent and NADP(H)-dependent SDRs are similar in human, mouse and plant, while the proportions of NAD(H)-dependent enzymes are much lower in fruit fly, worm and yeast. We show that, in spite of the great diversity of the SDR superfamily, the primary structure alone can be used for functional assignments and for predictions of coenzyme preference.
Culture of chondrocytes in fibroin-hydrogel sponge. (2003)

Fibroin-hydrogel sponge and collagen gel were used as scaffold for in vitro cartilage regeneration. Fibroin-hydrogel sponge was formed by phase separation from freezed fibroin solution. Chondrocytes were harvested from proximal humerus, distal femur and proximal tibia of 4-week-old Japanese white rabbits and inoculated in the fibroin-hydrogel sponge and collagen gel. Those constructs were cultured in DMEM supplemented with 10% FCS and 50 ml L-ascorbate at 37 degrees C. Histological observation, measurement of sulfated glycosaminoglycan and cell density were carried out at 3, 7, and 14 days after the cultivation. Well-defined cartilage tissue can be seen both in the fibroin-hydrogel sponge and in the collagen gel. The matrix was intensely stained by safranin-O and showed a metachromatic reaction in both group. However, the quantity of sulfated glycosaminoglycan and cell density of the fibroin-hydrogel sponge group were increased more rapidly than these of the collagen gel group. Thus, the chondrocytes proliferated in the fibroin sponge without losing their differentiated phenotype. It is possible that culture environment in the fibroin sponge was suitable for chondrocytes regeneration.
Antigen-presenting cells and the selection of immunodominant epitopes. (1997)

Cellular immune responses are directed against a narrow set of immunodominant peptides derived from complex antigens. By contrast, epitopes that are hidden or infrequent targets of immune responses have been termed cryptic or subdominant. Although the identification of immunodominant epitopes is important for vaccine development, understanding immunological reactivity to cryptic or subdominant epitopes may hold clues to autoimmunity. We have examined the role of antigen-presenting (APC) cells in the selection of class Ii-restricted epitopes for display to T lymphocytes. The formation and MHC-restricted presentation of distinct antigenic epitopes is directly dependent upon processing and ligand binding reactions within APC. A novel MHC heterodimer, HLA-DM, facilitates the binding and presentation of peptides by class II DR, DP, and DQ molecules. We have demonstrated that some epitopes derived from endogenous antigens bind class II proteins independent of DM, whereas the presentation of other endogenous peptides is greatly influenced by DM expression. Targeting of exogenous antigens into specialized processing compartments within APC appears to overcome the requirement for DM in antigen presentation. These studies suggest HLA-DM may play a role in epitope selection and immunodominance.
Proteolysis of Glucagon within Hepatic Endosomes by Membrane-associated Cathepsins B and D (1995)

The acidic glucagon-degrading activity of hepatic endosomes has been attributed to membrane-bound forms of cathepsins B and D. Endosomal lysates processed full-length nonradiolabeled glucagon to 32 different peptides that were identified by amino acid analysis and full-length sequencing. These indicated C-terminal carboxypeptidase, endopeptidase as well as N-terminal tripeptidyl-aminopeptidase activities in endosomes. Glucagon proteolysis was inhibited 95% by E-64 and pepstatin A, inhibitors of cathepsins B and D, respectively. This was confirmed by the pH 6-dependent chemical cross-linking of [125I]iodoglucagon to a polypeptide of 30 kDa, which was immunodepleted by polyclonal anti-cathepsin B antibody, and the removal of greater than 80% of glucagon-degrading activity by polyclonal antibodies to cathepsins B and D. By similar criteria, insulin-degrading enzyme was ruled out as a candidate enzyme for endosomal proteolysis of glucagon. Lysosomal contamination was unlikely since all forms of cathepsin B in endosomes, i.e. the major 45-kDa inactive precursor as well as the lesser amounts of the 32- and 28-kDa active forms, were tightly bound to endosomal membranes. Furthermore the mature 29-kDa single-chain and 22-kDa heavy-chain forms of cathepsin L were undetectable in endosomes, although high levels of the 37-kDa proform were observed. Membrane association of the cathepsins B and D was not to the mannose 6-phosphate receptor since association was unaffected by mannose 6-phosphate and/or EDTA, thereby indicating a distinct endosomal receptor. Hence, a pool of active cathepsins B and D as well as a poorly defined tripeptidyl aminopeptidase is maintained in endosomes by selective membrane retention. These hydrolases degrade glucagon internalized into liver parenchyma early in endocytosis.
An evaluation of current and alternative systems for quality grading carcasses of mature slaughter cows. (1998)

Strip loins from 354 female bovine carcasses, selected to represent 30 skeletal maturity (A, B, C, D, and E) x marbling score (SA/MA/AB, MD, MT, SM, SL, and TR/PD) subclasses, were used to evaluate current and alternative systems for classifying cow carcasses into expected-palatability groups. Strip loins were vacuum-packaged, stored for 14 d postmortem at 2 degrees C, and frozen (-27 degrees C). Five steaks from each strip loin, each cooked to a different internal temperature (60, 66, 71, 77, or 82 degrees C), were used for shear force determinations. Two steaks from each strip loin, one cooked to 66 degrees C and the other to 77 degrees C, were used for sensory evaluation. Increased carcass maturity was associated with decreased tenderness and juiciness, increased flavor intensity, and a higher incidence of flavors described as "painty," "fishy," and "grassy." Position of a carcass within a maturity group had a negligible effect on palatability. Increased marbling was associated with greater tenderness and juiciness, a lower incidence of steaks with a "grassy" flavor, and a higher incidence of steaks with a flavor described as "fatty." Relationships between marbling and beef palatability traits were consistent across all maturity groups. Carcasses of maturities A through E were most effectively stratified according to differences in palatability when marbling scores were grouped as follows: 1) MD and higher; 2) SL, SM, MT; and 3) TR/PD. Among mature (C, D, and E maturity) carcasses, yellow-colored fat was associated with greater beef toughness and higher detection rates for "grassy" and "fishy" flavors. Higher end-point temperatures were associated with higher shear force values and lower ratings for muscle fiber tenderness, connective tissue amount, overall tenderness, and juiciness. Two alternative grading approaches (one involving current quality grading factors and the other involving the use of fat color as an additional grade factor) were developed for possible use in classification of cow carcasses into expected-palatability groups. Both alternative systems provided a more effective stratification of cow carcasses according to palatability differences than did the current USDA quality grading system.