gebhart/patrepeval huggingface dataset:
Protein Secondary Structure Prediction (2009)

While the prediction of a native protein structure from sequence continues to remain a challenging problem, over the past decades computational methods have become quite successful in exploiting the mechanisms behind secondary structure formation. The great effort expended in this area has resulted in the development of a vast number of secondary structure prediction methods. Especially the combination of well-optimized/sensitive machine-learning algorithms and inclusion of homologous sequence information has led to increased prediction accuracies of up to 80%. In this chapter, we will first introduce some basic notions and provide a brief history of secondary structure prediction advances. Then a comprehensive overview of state-of-the-art prediction methods will be given. Finally, we will discuss open questions and challenges in this field and provide some practical recommendations for the user.
Computing geodesics and minimal surfaces via graph cuts (2003)

Geodesic active contours and graph cuts are two standard image segmentation techniques. We introduce a new segmentation method combining some of their benefits. Our main intuition is that any cut on a graph embedded in some continuous space can be interpreted as a contour (in 2D) or a surface (in 3D). We show how to build a grid graph and set its edge weights so that the cost of cuts is arbitrarily close to the length (area) of the corresponding contours (surfaces) for any anisotropic Riemannian metric. There are two interesting consequences of this technical result. First, graph cut algorithms can be used to find globally minimum geodesic contours (minimal surfaces in 3D) under arbitrary Riemannian metric for a given set of boundary conditions. Second, we show how to minimize metrication artifacts in existing graph-cut based methods in vision. Theoretically speaking, our work provides an interesting link between several branches of mathematics -differential geometry, integral geometry, and combinatorial optimization. The main technical problem is solved using Cauchy-Crofton formula from integral geometry.
Guard Cell Signal Transduction Network: Advances in Understanding Abscisic Acid, CO2, and Ca2+Signaling (2010)

Stomatal pores are formed by pairs of specialized epidermal guard cells and serve as major gateways for both CO(2) influx into plants from the atmosphere and transpirational water loss of plants. Because they regulate stomatal pore apertures via integration of both endogenous hormonal stimuli and environmental signals, guard cells have been highly developed as a model system to dissect the dynamics and mechanisms of plant-cell signaling. The stress hormone ABA and elevated levels of CO(2) activate complex signaling pathways in guard cells that are mediated by kinases/phosphatases, secondary messengers, and ion channel regulation. Recent research in guard cells has led to a new hypothesis for how plants achieve specificity in intracellular calcium signaling: CO(2) and ABA enhance (prime) the calcium sensitivity of downstream calcium-signaling mechanisms. Recent progress in identification of early stomatal signaling components are reviewed here, including ABA receptors and CO(2)-binding response proteins, as well as systems approaches that advance our understanding of guard cell-signaling mechanisms.
<title>Integrated-optic lossless beamsplitters</title> (2000)

Erbium-doped thin-film waveguides are promising as loss-compensating devices for various photonic integrated circuits. We have addressed major challenges in the development of lossless splitters based on the Er-doped glass films: the requirement of high Er concentrations, the fabrication of quality waveguides, and the development of suitable architectures for beamsplitting and for signal and pump combining and separating, and the limitations of maximum-obtainable gain of Er-doped thin-film amplifiers. Based on these results, we have successfully developed integrated-optic, lossless splitters. The fabricated devices clearly demonstrate lossless transmission of an optical signal at 1.54 (mu) m wavelength through a 1x2 splitter and an Er-doped amplifier that are monolithically integrated on the same substrate.
Photovoltaic detection of infrared light in a GaAs/AlGaAs superlattice (1988)

We report the observation of photovoltaic infrared photodetection in an n-type GaAs/AlGaAs superlattice within the optical range 3.6–6.2 μm. A built-in graded AlGaAs barrier (∼0.2 eV) provides charge polarization in the sample by allowing the optically excited electrons in the second miniband of the superlattice to diffuse over this barrier. The optical polarization of the infrared signal is consistent with the selection rules applicable to the superlattice. The infrared photoresponse results from first-to-second miniband as well as shallow donor-to-second miniband photoexcitations within the superlattice. Donor-to-second miniband photoexcitation is dominant at low temperatures (&amp;lt;25 K).
A Plasma Membrane Wound Proteome (2010)

Cells in mechanically active tissues undergo constant plasma membrane damage that must be repaired to allow survival. To identify wound-associated proteins, a cell-impermeant, thiol-reactive biotinylation reagent was used to label and subsequently isolate intracellular proteins that become exposed on the surface of cultured cells after plasma membrane damage induced by scraping from substratum or crushing with glass beads. Scrape-damaged cells survived injury and were capable of forming viable colonies. Proteins that were exposed to the cell surface were degraded or internalized a few seconds to several minutes after damage, except for vimentin, which was detectable on the cell surface for at least an hour after injury. Seven major biotinylated protein bands were identified on SDS-PAGE gels. Mass spectrometric studies identified cytoskeletal proteins (caldesmon-1 and vimentin), endoplasmic reticulum proteins (ERp57, ERp5, and HSP47), and nuclear proteins (lamin C, heterogeneous nuclear ribonucleoprotein F, and nucleophosmin-1) as major proteins exposed after injury. Although caldesmon was a major wound-associated protein in calpain small subunit knock-out fibroblasts, it was rapidly degraded in wild-type cells, probably by calpains. Lamin C exposure after wounding was most likely the consequence of nuclear envelope damage. These studies document major intracellular proteins associated with the cell surface of reversibly damaged somatic cells. The studies also show that externalization of some proteins reported to have physiologic or pathologic roles on the cell surface can occur in cells undergoing plasma membrane damage and subsequent repair.
Inhibitors of the mitotic kinesin spindle protein (2004)

AbstractSmall molecule inhibitors of kinesin spindle protein (KSP), a kinesin essential to mitotic spindle formation, arrest cell cycle progression and the proliferation of tumour cells in vitro and in vivo, and thus demonstrate potential as novel antimitotic agents. Recently, KSP inhibitors of wide structural diversity have appeared in the patent literature. This review covers issued patents and patent applications that disclose novel small molecule inhibitors of the mitotic kinesin KSP that appeared between 2001 and July 2004.Keywordsanti-mitoticcancerkinesin spindle protein (KSP)mitotic kinesin
Th1 Cytokine Patterns in Cervical Human Papillomavirus Infection (1999)

The host's immune response to cervical human papillomavirus (HPV) infection is poorly understood. In a longitudinal cohort of women with cervical HPV infections, defined by PCR-based HPV DNA testing, we used exfoliated cervical cells and reverse transcription-PCR to examine the cervical mucosal mRNA expression of cytokines involved in regulating cell-mediated immunity. We identified seven HPV-positive subjects who were found to have cleared their HPV infections 4 months later. In all seven, a T-helper type 1 (Th1) cytokine pattern (expression of gamma interferon and absence of interleukin-4) preceded clearance. The more variable cytokine patterns seen in HPV-negative subjects suggest that the Th1 pattern in the women with subsequent clearance was a response to the HPV infection. This contention is supported by additional cross-sectional data showing a Th1 pattern in a majority of HPV-positive women. This study establishes a feasible means for assessing local cytokine expression in the cervical milieu and demonstrates that a Th1 cytokine response is associated with subsequent clearance of cervical HPV infection.
O-307 Cannabidiol as a potential novel treatment for endometriosis by its anti-inflammatory and anti-oxidative effects in an experimental rat model (2022)

Abstract Study question Can cannabidiol (CBD) - a nonpsychoactive constituent of the cannabis plant – be used in the treatment of endometriosis by its anti-inflammatory and anti-oxidative effects? Summary answer CBD appears to be a potential novel therapeutic agent in the treatment of endometriosis through inhibiting inflammation and decreasing oxidative stress in a dose-dependent manner. What is known already The endocannabinoid system (ECS) consists of various bioactive lipids that are produced endogenously which activate cannabinoid 1-2 receptors (CB1-2). Alterations in ECS are associated with many physiological and pathological conditions throughout the body including endometriosis. The events that play role in the development and growth of ectopic endometriotic implants are proliferation, angiogenesis, and inflammation. By their anti-inflammatory and anti-oxidative effects, phyto and synthetic cannabinoids had been investigated and started being used for diseases with similar mechanisms. CBD is a nonpsychoactive constituent of the cannabis plant which acts indirectly upon the CB-1 receptor and as an inverse agonist of CB-2 receptor. Study design, size, duration Endometrial implants were surgically induced in 36 female Wistar-Albino rats in the first surgery. After confirmation of endometriotic foci in the second surgery, the rats were randomized into four groups. Group 1 (leuprolide acetate group) was given a single 1 mg/kg subcutaneous injection of leuprolide acetate. Groups 2,3 and 4 were 5 mg/kg CBD, saline solution (control group), and 20 mg/kg CBD injected groups, respectively, and daily intra-peritoneal (i.p.) injections were applied for seven days. Participants/materials, setting, methods After 21 days from the second surgery, the rats were sacrificed and histopathological analysis of endometriotic lesions, total antioxidant status (TAS), total oxidant status (TOS), oxidative stress index (OSI), interleukin 1 (IL-1), interleukin 6 (IL-6) and tumor necrosis factor-alpha (TNF-a) measurements in blood and peritoneal fluid samples, and immunohistochemical staining for TNF-a expression in endometriotic tissue were evaluated. Main results and the role of chance After treatment, significant reductions in TOS, OSI, IL-1, IL-6 and TNF-α levels in the blood and peritoneal fluid samples and TNF-α expression of endometriotic implants (p &amp;lt; 0.01) and increased TAS (p &amp;lt; 0.01) were found in the CBD 5mg/kg and leuprolide acetate groups. Limitations, reasons for caution The limitation is that this is an experimental rat model study. Wider implications of the findings This is the first study in the literature that evaluates the effects of a phytocannabinoid -CBD- on endometriosis in a rat model. With its anti-inflammatory and anti-oxidative effects and favorable safety and tolerability profile, it might be a candidate for a novel treatment in endometriosis. Trial registration number not applicable
Myocardial imaging agents: Synthesis, characterization and evaluation of [(Z) and (Z,E)‐(1‐[82br]bromo‐1‐penten‐5‐yl)]triphenylphosphonium cations (1990)

Abstract The phosphonium compounds, [(Z) and (Z/E)‐(1‐bromo‐1‐penten‐5‐yl)]triphenylphosphonium iodides (yield, 65–70%) and the corresponding bromine‐82‐labeled analogues have been prepared as potential myocardial imaging agents. The 2/1 isomer composition of the Z/E mixture has been confirmed by single crystal X‐ray analysis. The radiobrominated (Z)‐isomer and (Z/E)‐mixture both show high heart uptake and high heart/blood ratios in rats. These data suggest that the bromine‐75 and bromine‐76‐labeled agents could be good candidates for myocardial imaging using positron emission computed tomography.
Biophysical Characterization of Interactions Involving Importin-α during Nuclear Import (2001)

Proteins containing the classical nuclear localization sequences (NLSs) are imported into the nucleus by the importin-alpha/beta heterodimer. Importin-alpha contains the NLS binding site, whereas importin-beta mediates the translocation through the nuclear pore. We characterized the interactions involving importin-alpha during nuclear import using a combination of biophysical techniques (biosensor, crystallography, sedimentation equilibrium, electrophoresis, and circular dichroism). Importin-alpha is shown to exist in a monomeric autoinhibited state (association with NLSs undetectable by biosensor). Association with importin-beta (stoichiometry, 1:1; K(D) = 1.1 x 10(-8) m) increases the affinity for NLSs; the importin-alpha/beta complex binds representative monopartite NLS (simian virus 40 large T-antigen) and bipartite NLS (nucleoplasmin) with affinities (K(D) = 3.5 x 10(-8) m and 4.8 x 10(-8) m, respectively) comparable with those of a truncated importin-alpha lacking the autoinhibitory domain (T-antigen NLS, K(D) = 1.7 x 10(-8) m; nucleoplasmin NLS, K(D) = 1.4 x 10(-8) m). The autoinhibitory domain (as a separate peptide) binds the truncated importin-alpha, and the crystal structure of the complex resembles the structure of full-length importin-alpha. Our results support the model of regulation of nuclear import mediated by the intrasteric autoregulatory sequence of importin-alpha and provide a quantitative description of the binding and regulatory steps during nuclear import.
Udenafil: efficacy and tolerability in the management of erectile dysfunction (2012)

Udenafil is a potent novel phosphodiesterase-5 inhibitor approved for use in Korea. Udenafil has unique properties, with a T max of 1.0-1.5 h and a T 1/2 of 11-13 h (a relatively rapid onset and a long duration of action). Therefore, both on-demand and once-daily use of udenafil have been reported. Udenafil's efficacy and tolerability have been evaluated in several studies, and recent and continuing studies have demonstrated udenafil's promise in both dosing regimens. Presently, tadalafil is the only FDA-approved drug for daily dosing, but udenafil can be used as a once-daily dose for erectile dysfunction patients who cannot tolerate tadalafil due to phosphodiesterase subtype selectivity. Udenafil as an on-demand or once-daily dose is effective and tolerable, but more studies are needed in patients of other ethnicities and with comorbid conditions such as diabetes mellitus, hypertension, and benign prostate hyperplasia.
Induction of macrophage antitumor activity by acetylated low density lipoprotein containing lipophilic muramyl tripeptide. (1988)

A method has been developed for the selective delivery of lipophilic immunomodulators to macrophages, which results in the induction of antitumor activity. This method utilizes exhaustively acetylated low density lipoprotein (acetyl-LDL) to deliver the lipophilic immunomodulator, muramyl tripeptide phosphatidylethanolamine (MTP-PtdEtn; amide composed of N-acetylmuramyl-L-alanyl-D-isoglutamyl-L-alanine and dipalmitoyl phosphatidylethanolamine) to macrophages (M phi) by means of a scavenger lipoprotein receptor pathway. The binding of acetyl-LDL:MTP-PtdEtn to M phi showed specificity since minimal competition was observed in the presence of excess native LDL or phosphatidylcholine/cholesterol liposomes. Additional binding studies showed that acetyl-LDL may serve as a suitable delivery vehicle to a wide variety of M phi in different stages of activation. Cytostatic and tumoricidal activities by thioglycolate-elicited M phi against two tumor cell lines were examined in vitro following incubation with the acetyl-LDL:MTP-PtdEtn complex. Cytostatic activity against B16F10 melanoma cells was induced after the incubation of thioglycolate-elicited M phi with a minimum of 25 micrograms of acetyl-LDL protein containing 2.5 micrograms of bound MTP-PtdEtn (approximately equal to 40 molecules per particle of acetyl-LDL). The induction of cytostasis was not affected by liposome bilayers, which were also endocytosed by the M phi. In addition, tumoricidal activity against P815 mastocytoma cells was demonstrated at a 40:1 effector-to-target ratio using 18 micrograms of the acetyl-LDL:MTP-PtdEtn complex containing 3.6 micrograms of MTP-PtdEtn (approximately equal to 80 molecules per particle). These studies describe a method for the induction of antitumor activity by use of a chemically modified serum component, acetyl-LDL, to direct lipophilic immunomodulators to M phi.
Working Set Selection Using Second Order Information for Training Support Vector Machines (2005)

Working set selection is an important step in decomposition methods for training support vector machines (SVMs). This paper develops a new technique for working set selection in SMO-type decomposition methods. It uses second order information to achieve fast convergence. Theoretical properties such as linear convergence are established. Experiments demonstrate that the proposed method is faster than existing selection methods using first order information.
Next cache line and set prediction (1995)

Accurate instruction fetch and branch prediction is increasingly important on today's wide-issue architectures. Fetch prediction is the process of determining the next instruction to request from the memory subsystem. Branch prediction is the process of predicting the likely out-come of branch instructions. Several researchers have proposed very effective fetch and branch prediction mechanisms including branch target buffers (BTB) that store the target addresses of taken branches. An alternative approach fetches the instruction following a branch by using an index into the cache instead of a branch target address. We call such an index a next cache line and set (NLS) predictor. A NLS predictor is a pointer into the instruction cache, indicating the target instruction of a branch.In this paper we examine the use of NLS predictors for efficient and accurate fetch and branch prediction. Previous studies associated each NLS predictor with a cache line and provided only one-bit conditional branch predictors. Our study examines the use of NLS predictors with highly accurate two-level correlated conditional branch architectures. We examine the performance of decoupling the NLS predictors from the cache line and storing them in a separate tag-less memory buffer. Our results show that the decoupled architecture performs better than associating the NLS predictors with the cache line, that the NLS architecture benefits from reduced cache miss rates, and it is particularly effective for programs containing many branches. We also provide an in-depth comparison between the NLS and BTB architectures, showing that the NLS architecture is a competitive alternative to the BTB design.
Writing from within the contact zone (2011)

The Contact Zone! It makes me think of the one unit of Philosophy I did in my Arts degree where we studied an idea that every relationship is a power struggle; a conflict. I can't remember the theorist, it may have been Kant but I'm not sure. It goes against ideas about harmony - perhaps it is more the nature of the conflict rather than its outcome that is the single, most important element in forming relationships.The Contact Zone reminds me of this constant battle for dominance in relationships.
Synthesis of substituted 3‐amino‐4‐cyano‐1‐oxo‐1,2,5,10‐tetrahydroazepino [3,4‐b]indoles (1997)

Abstract The preparation of 3‐amino‐ and 3‐dialkylamino‐4‐cyanoazepino[3,4‐fc]indoles bearing substituents on the aromatic nucleus and N 10 is outlined. Starting from suitable substituted ethyl 3‐formylindole‐2‐carboxy‐latcs 2 , condensation with malononitrile ( 3 ) and subsequent sodium borohydride‐reduction yielded ethyl 3‐(2,2‐dicyanoethyl)indole‐2‐carboxylates 5 and 19 , respectively, which were cyclized in boiling alkoxides to 3‐alkoxy‐4‐cyanoazepino[3,4‐ b ]indoles 10,11,20 and 21 . This sequence constitutes a novel and flexible route to functional azepino[3,4‐ b &gt;]indoles. The aminolysis of 10,11,20 and 21 with different amines and ammonia yielded the title compounds which were screened for their possible biological activity.
Language without communication: a case study (1979)

ABSTRACT Two branches of language functioning are now actively being studied: one focuses on language as a system for expressing syntactic-semantic relations, the other as a system of interpersonal communication. In this paper, a case is presented of a child who at 3; 3 showed a marked schism between these two areas. In the former domain he displayed behaviour that in most respects was age appropriate and relatively extensive. In the latter domain, he displayed almost totally ineffective functioning. His difficulties in the use of language for communication were mirrored from infancy by a serious failure either to understand or produce non-verbal communication (e.g. gestures). It is suggested that the structural and communicative aspects of language are based upon different sets of skills which particularly in cases of language disorder may function independently of one another.
Phosphine-Free Palladium Acetate Catalyzed Suzuki Reaction in Water (2005)

Pd(OAc)(2) in a mixture of water and poly(ethylene glycol) (PEG) is shown to be an extremely active catalyst for the Suzuki reaction of aryl iodides and bromides. The reaction can be conducted under mild conditions (50 degrees C) without the use of a microwave or phosphine ligand in high yields. The isolation of the products is readily performed by the extraction of diethyl ether, and the Pd(OAc)(2)-PEG can be reused without significant loss in activity.
Beta-amyloid precursor protein of Alzheimer disease occurs as 110- to 135-kilodalton membrane-associated proteins in neural and nonneural tissues. (1988)

Progressive cerebral deposition of extracellular filaments composed of the beta-amyloid protein (beta AP) is a constant feature of Alzheimer disease (AD). Since the gene on chromosome 21 encoding the beta AP precursor (beta APP) is not known to be altered in AD, transcriptional or posttranslational changes may underlie accelerated beta AP deposition. Using two antibodies to the predicted carboxyl terminus of beta APP, we have identified the native beta APP in brain and nonneural human tissues as a 110- to 135-kDa protein complex that is insoluble in buffer and found in various membrane-rich subcellular fractions. These proteins are relatively uniformly distributed in adult brain, abundant in fetal brain, and detected in nonneural tissues that contain beta APP mRNA. Similarly sized proteins occur in rat, cow, and monkey brain and in cultured human HL-60 and HeLa cells; the precise patterns in the 110- to 135-kDa range are heterogeneous among various tissues and cell lines. Confirmation that the immunodetected tissue proteins are forms of beta APP was obtained when mammalian cells transfected with a full-length beta APP cDNA showed selectively augmented expression of 110- to 135-kDa proteins and specific immunocytochemical staining. Unexpectedly, the antibodies to the carboxyl terminus of beta APP labeled amyloid-containing senile plaques in AD brain. We conclude that the highly conserved beta APP molecule occurs in mammalian tissues as a heterogeneous group of membrane-associated proteins of approximately 120 kDa. Detection of the nonamyloidogenic carboxyl terminus within plaques suggests that proteolytic processing of the beta APP into insoluble filaments occurs locally in cortical regions that develop beta-amyloid deposits with age.