gebhart/patrepeval huggingface dataset:
Helix stabilization by Glu-...Lys+ salt bridges in short peptides of de novo design. (1987)

Four alanine-based peptides were designed, synthesized, and tested by circular dichroism for alpha-helix formation in H2O. Each peptide has three glutamic/lysine residue pairs, is 16 or 17 amino acids long, and has blocked alpha-NH2 and alpha-COOH groups. In one set of peptides ("i+4"), the glutamic and lysine residues are spaced 4 residues or 1 residue apart. In the other set ("i+3"), the spacing is 3 or 2 residues. Within each of these sets, a pair of peptides was made in which the positions of the glutamic and lysine residues are reversed [Glu, Lys (E,K) vs. Lys, Glu (K,E)] in order to assess the interaction of the charged side chains with the helix dipole. Since the amino acid compositions of these peptides differ at most by a single alanine residue, differences in helicity are caused chiefly by the spacing and positions of the charged residues. The basic aim of this study was to test for helix stabilization by (Glu-, Lys+) ion pairs or salt bridges (H-bonded ion pairs). The results are as follows. (i) All four peptides show significant helix formation, and the stability of the alpha-helix does not depend on peptide concentration in the range studied. The best helix-former is (i+4)E,K, which shows approximately 80% helicity in 0.01 M NaCl at pH 7 and 0 degree C. (ii) The two i+4 peptides show more helix formation than the i+3 peptides. pH titration gives no evidence for helix stabilization by i+3 ion pairs. (iii) Surprisingly, the i+4 peptides form more stable helices than the i+3 peptides at extremes of pH (pH 2 and pH 12) as well as at pH 7. These results may be explained by helix stabilization through Glu-...Lys+ salt bridges at pH 7 and singly charged H bonds at pH 2 (Glu0...Lys+) and pH 12 (Glu-...Lys0). The reason why these links stabilize the alpha-helix more effectively in the i+4 than in the i+3 peptides is not known. (iv) Reversal of the positions of glutamic and lysine residues usually affects helix stability in the manner expected for interaction of these charged groups with the helix dipole. (v) alpha-Helix formation in these alanine-based peptides is enthalpy-driven, as is helix formation by the C-peptide of ribonuclease A.
Educational assortative mating across marriage markets: Nonhispanic whites in the United States (2000)

Whether local marriage market conditions shape marriage behavior is a central social demographic question. Most work on this subject, however, focuses on one type of market condition--sex ratios--and on a single outcome--marital timing or sorting. We examine the impact of local marriage markets' educational composition on educational assortative mating and on how sorting varies with age. We estimate a discrete-time competing-risks model of educational sorting outcomes, using individual data from the NLSY and community descriptors aggregated from census microdata. Results show that residents of educationally less favorable marriage markets are more likely to marry down on education, and that (for women) their chance of doing so increases with age more than for residents of more favorable markets.
On Calibration of Modern Neural Networks (2017)

Confidence calibration -- the problem of predicting probability estimates representative of the true correctness likelihood -- is important for classification models in many applications. We discover that modern neural networks, unlike those from a decade ago, are poorly calibrated. Through extensive experiments, we observe that depth, width, weight decay, and Batch Normalization are important factors influencing calibration. We evaluate the performance of various post-processing calibration methods on state-of-the-art architectures with image and document classification datasets. Our analysis and experiments not only offer insights into neural network learning, but also provide a simple and straightforward recipe for practical settings: on most datasets, temperature scaling -- a single-parameter variant of Platt Scaling -- is surprisingly effective at calibrating predictions.
Release of γ-Aminobutyric Acid in the Dorsal Horn and Suppression of Tactile Allodynia by Spinal Cord Stimulation in Mononeuropathic Rats (1996)

Our results indicate that the development of allodynia, a common symptom in neuropathic pain states, may be linked to a decreased spinal release of GABA. We suggest that an SCS-induced release of GABA could be important for the suppression of allodynia observed in rats after SCS. Similar mechanisms could also be involved in the SCS-induced alleviation of pain in patients with peripheral neuropathy.
Effect of different crossbreeds on chemical and sensory profiling of Istrian dry-cured ham (2010)

An investigation has been carried out on the effect of different crossbreeds on chemical and sensory profiling of Croatian representative pork products, Istrian hams. Due to the original trimming of hams (without skin and subcutaneous adipose tissue) the total weight loss was significantly higher (41.67–43.69%) in all three genotypes (Swedish Landrace×Dutch Large Whit ×Pietrain (SL×DLW×P), Dutch Large White×Swedish Landrace (DLW×SL) and Dutch Large White×Duroc (DLW×D)) in comparison with the Italian and Spanish hams with skin and subcutaneous adipose tissue. Hams from DLW×D genotype had a significantly lower (P 0.05). The cholesterol level is low (541.9–555.9 mg kg−1), which makes Istrian dry-cured ham a dietary product. Hams from DLW×D had...
Increased Frequencies of Allergen‐Induced Interleukin‐13‐Producing Cells in Atopic Individuals During the Pollen Season (1998)

We have reported previously that allergen-specific serum IgE levels were correlated with allergen-induced interleukin (IL)-4 in type I allergic individuals. Here, we wanted to investigate whether IL-13, another switch factor for IgE, was induced by allergen in vitro and if so, whether this was correlated with the elevated serum IgE-levels seen in atopic individuals, and whether the cytokine profile changed during pollen season. Peripheral blood mononuclear cells from 14 atopic and 14 healthy individuals collected out of the pollen season were incubated in vitro with allergens (birch or timothy) and the number of IL-4, IL-13, IL-10 and IFN-gamma producing cells was determined by ELISPOT. In response to the specific allergen, IL-13-producing cells were seen in allergic but not in healthy individuals. The number of IL-13-producing cells was significantly correlated with the allergen-specific serum IgE levels. When the allergic individuals were tested during the pollen season, the number of allergen-specific IL-4- and IL-13-producing cells, as well as serum levels of specific IgE, increased. The IL-13 increase seen in ELISPOT was confirmed by a RT-PCR assay. No seasonal changes were seen in response to purified protein derivative (PPD) or the mitogen PHA. During the pollen season, the IL-4 and IL-13 responses were highly correlated. Taken together, our results support the roles of both IL-13 and IL-4 in the regulation of allergen-specific IgE levels in atopic individuals.
Cutting edge: identification of the orphan chemokine receptor GPR-9-6 as CCR9, the receptor for the chemokine TECK. (1999)

Thymus-expressed chemokine (TECK) has been reported to chemoattract dendritic cells, thymocytes, and activated macrophages. Here, we show that TECK is a specific agonist for a human orphan receptor called GPR-9-6. We have determined the cDNA sequence of human GPR-9-6 and cloned the corresponding murine cDNA. Human and murine GPR-9-6 expression is very high in the thymus and low in lymph nodes and spleen. RT-PCR analysis of murine GPR-9-6 expression on murine FACS-sorted thymocyte subpopulations showed that this gene is expressed in both immature and mature T cells. Additions of human or murine TECK to HEK 293/human GPR-9-6 and HEK 293/murine GPR-9-6 transfectants provoked intracytoplasmic calcium mobilization. Human TECK also induced the in vitro migration of HEK 293/human GPR-9-6 cells. These results confirm that GPR-9-6 is a specific receptor for TECK. According to the established nomenclature system, we propose to rename GPR-9-6 as CC chemokine receptor 9 (CCR9).
Does vestibular stimulation activate thalamocortical mechanisms that reintegrate impaired cortical regions? (1999)

Caloric stimulation induced a transient reversal of multimodal hemispatial cognitive deficits in an 81-year-old woman with an acute left cerebral hemisphere stroke. The patient had unawareness of her right hand (asomatognosia), right-sided visual unawareness (hemineglect), aphasia and right-sided weakness (hemiplegia) prior to the stimulation. Transient improvements in impaired sensory, motor, linguistic and cognitive function developed within 30 s following application of the caloric stimulus and onset of horizontal nystagmus. The effect persisted for 3 min and ceased completely after 5 min. While several recent reports have described the capacity of caloric stimulation to transiently improve or reverse a wide range of attentional, cognitive and motor impairments, most examples are in right-hemisphere-damaged patients with long-standing brain injury. Typically, patients have been tested several months or years after the onset of the deficit. A possible mechanism for the temporary reintegration of multiple cognitive functions in this patient is discussed.
Iterative estimation and cancellation of clipping noise for OFDM signals (2003)

Clipping is an efficient and simple method to reduce the peak-to-average power ratio (PAPR) of orthogonal frequency division multiplexing (OFDM) signals. However, clipping causes distortion and out-of-band radiation. In this letter, a novel iterative receiver is proposed to estimate and cancel the distortion caused by clipping noise. The proposed method is applied to clipped and filtered OFDM signals. It is shown by simulation that for an IEEE 802.11a typical scenario the system performance can be restored to within 1 dB of the nonclipped case with only moderate complexity increase and with no bandwidth expansion.
A multi-frequency microstrip-fed annular slot antenna (2002)

A single feed multi-frequency annular slot antenna is analyzed with an integral equation program and experimentally. Experimental impedance bandwidths of the first three operating frequencies range from 6.6 to 10.8 percent. At these frequencies, the antenna displays a broadside bi-directional radiation pattern, with directivity on the order of 5 dB. Tuning the antenna is examined by changing the width of the slot ring and adjusting the open-circuited microstrip feed line.
Helix Formation in the Polymer Brush (2011)

This work considers the physics of a brush formed by polymers capable of undergoing a helix-coil transition. A self-consistent field approximation for strongly stretched polymer chains is used in combination with a lattice model of the interaction energy in helix-coil mixtures. Crowding-induced chain stretching stabilizes helix formation at moderate tethering densities while high tethering density causes sufficiently strong stretching to unravel segments of the helix, resulting in distinct layers of monomer density and helical content. Compared to a random-coil brush at low-to-moderate tethering density, a helicogenic brush is less resistant to compression in the direction perpendicular to stretching due to easy alignment of helices and fewer unfavorable interactions between helical segments. At higher tethering density, the abovementioned stretch-induced decrease in helical content resists further compression. The proposed model is useful for understanding an emerging class of biomaterials that utilize helix-forming polymer brushes to induce shape changes or to stabilize biofunctional helical peptide sequences.
Heparin Structure and Interactions with Basic Fibroblast Growth Factor (1996)

Crystal structures of heparin-derived tetra- and hexasaccharides complexed with basic fibroblast growth factor (bFGF) were determined at resolutions of 1.9 and 2.2 angstroms, respectively. The heparin structure may be approximated as a helical polymer with a disaccharide rotation of 174 degrees and a translation of 8.6 angstroms along the helix axis. Both molecules bound similarly to a region of the bFGF surface containing residues asparagine-28, arginine-121, lysine-126, and glutamine-135, the hexasaccharide also interacted with an additional binding site formed by lysine-27, asparagine-102, and lysine-136. No significant conformational change in bFGF occurred upon heparin oligosaccharide binding, which suggests that heparin primarily serves to juxtapose components of the FGF signal transduction pathway.
The past, present and future of opioid withdrawal assessment: a scoping review of scales and technologies (2019)

It is timely to investigate how opioid withdrawal scales can be complemented or replaced with reliable monitoring technologies. Use of noninvasive wearable sensors to continuously monitor physiologic changes associated with opioid withdrawal represents a potential to extend monitoring outside clinical setting.
Human neutrophil lipocalin (HNL) as a diagnostic tool in children with acute infections: A study of the kinetics (2005)

HNL is a promising diagnostic tool in the distinction of acute infections caused by bacteria or virus. The differences in the kinetics of CRP and HNL make HNL a better marker for monitoring antibacterial treatment, since HNL is probably elevated only when an active bacterial infection is at hand.
Relationship Between the Occurrence of Cysteine in Proteins and the Complexity of Organisms (2000)

The occurrence and relative positions of cysteine residues were investigated in proteins of various species. Considering random mathematical occurrence for an amino acid coded by two codons (3. 28%), cysteine is underrepresented in all organisms investigated. Representation of cysteine appears to correlate positively with the complexity of the organism, ranging between 2.26% in mammals and 0. 5% in some members of the Archeabacteria order. This observation, together with the results obtained from comparison of cysteine content of various ribosomal proteins, indicates that evolution takes advantage of increased use of cysteine residues. In all organisms studied except plants, two cysteines are frequently found two amino acid residues apart (C-(X)(2)-C motif). Such a motif is known to be present in a variety of metal-binding proteins and oxidoreductases. Remarkably, more than 21% of all of cysteines were found within the C-(X)(2)-C motifs in ARCHEA.: This observation may indicate that cysteine appeared in ancient metal-binding proteins first and was introduced into other proteins later.
Copy-up mutants of the plasmid RK2 replication initiation protein are defective in coupling RK2 replication origins. (1996)

The broad host range plasmid RK2 replicates and regulates its copy number in a wide range of Gram-negative bacteria. The plasmid-encoded trans-acting replication protein TrfA and the origin of replication oriV are sufficient for controlled replication of the plasmid in all Gram-negative bacteria tested. The TrfA protein binds specifically to direct repeat sequences (iterons) at the origin of replication. A replication control model, designated handcuffing or coupling, has been proposed whereby the formation of coupled TrfA-oriV complexes between plasmid molecules results in hindrance of origin activity and, consequently, a shut-down of plasmid replication under conditions of higher than normal copy number. Therefore, according to this model, the coupling activity of an initiation protein is essential for copy number control and a copy-up initiation protein mutant should have reduced ability to form coupled complexes. To test this model for plasmid RK2, two previously characterized copy-up TrfA mutations, trfA-254D and trfA-267L, were combined and the resulting copy-up double mutant TFrfA protein TrfA-254D/267L was characterized. Despite initiating runaway (uncontrolled) replication in vivo, the copy-up double-mutant TrfA protein exhibited replication kinetics similar to the wild-type protein in vitro. Purified TrfA-254D, TrfA-267L, and TrfA-254D/267L proteins were then examined for binding to the iterons and for coupling activity using an in vitro ligase-catalyzed multimerization assay. It was found that both single and double TrfA mutant proteins exhibited substantially reduced (single mutants) or barely detectable (double mutant) levels of coupling activity while not being diminished in their capacity to bind to the origin of replication. These observations provide direct evidence in support of the coupling model of replication control.
Assessing the Probability That a Positive Report is False: An Approach for Molecular Epidemiology Studies (2004)

Too many reports of associations between genetic variants and common cancer sites and other complex diseases are false positives. A major reason for this unfortunate situation is the strategy of declaring statistical significance based on a P value alone, particularly, any P value below.05. The false positive report probability (FPRP), the probability of no true association between a genetic variant and disease given a statistically significant finding, depends not only on the observed P value but also on both the prior probability that the association between the genetic variant and the disease is real and the statistical power of the test. In this commentary, we show how to assess the FPRP and how to use it to decide whether a finding is deserving of attention or "noteworthy." We show how this approach can lead to improvements in the design, analysis, and interpretation of molecular epidemiology studies. Our proposal can help investigators, editors, and readers of research articles to protect themselves from overinterpreting statistically significant findings that are not likely to signify a true association. An FPRP-based criterion for deciding whether to call a finding noteworthy formalizes the process already used informally by investigators--that is, tempering enthusiasm for remarkable study findings with considerations of plausibility.
Nonmetal Catalyzed Insertion Reactions of Diazocarbonyls to Acid Derivatives in Fluorinated Alcohols (2011)

The insertion reaction of diazocarbonyls to acids could be performed smoothly in fluorinated alcohols in the absence of metal catalyst. This new procedure allowed the chemoselective preparation of various functionalized compounds such as acyloxyesters, depsipeptides, and sulfonate, phosphonate, or boronate derivatives.
Therapeutic angiogenesis for patients with limb ischemia by utilization of fibrin meshwork. Pilot randomized controlled study. (2003)

IM injection of fibrin is safe and appears to be an efficient method to treat limb ischemia. These findings indicate that use of fibrin may be a novel and simple method for inducing therapeutic angiogenesis.
A Mutant D‐Fructose‐6‐Phosphate Aldolase (Ala129Ser) with Improved Affinity towards Dihydroxyacetone for the Synthesis of Polyhydroxylated Compounds (2010)

Abstract A mutant of D ‐fructose‐6‐phosphate aldolase (FSA) of Escherichia coli , FSA A129S, with improved catalytic efficiency towards dihydroxyacetone (DHA), the donor substrate in aldol addition reactions, was explored for synthetic applications. The k cat / K M value for DHA was 17‐fold higher with FSA A129S than that with FSA wild type (FSA wt ). On the other hand, for hydroxyacetone as donor substrate FSA A129S was found to be 3.5‐fold less efficient than FSA wt . Furthermore, FSA A129S also accepted glycolaldehyde (GA) as donor substrate with 3.3‐fold lower affinity than FSA wt . This differential selectivity of both FSA wt and FSA A129S for GA makes them complementary biocatalysts allowing a control over donor and acceptor roles, which is particularly useful in carboligation multi‐step cascade synthesis of polyhydroxylated complex compounds. Production of the mutant protein was also improved for its convenient use in synthesis. Several carbohydrates and nitrocyclitols were efficiently prepared, demonstrating the versatile potential of FSA A129S as biocatalyst in organic synthesis.
Therapeutic Applications of Nucleic Acids and Their Analogues in Toll-like Receptor Signaling (2012)

Toll-like receptors (TLRs) belong to a family of innate immune receptors that detect and clear invading microbial pathogens. Specifically intracellular TLRs such as TLR3, TLR7, TLR8 and TLR9 recognize nucleic acids such as double-stranded RNA, single-stranded RNA and CpG DNA respectively derived from microbial components. Upon infection, nucleic acid sensing TLRs signal within endosomal compartment triggering the induction of essential proinflammatory cytokines and type I interferons to initiate innate immune responses thereby leading to a critical role in the development of adaptive immune responses. Thus, stimulation of TLRs by nucleic acids is a promising area of research for the development of novel therapeutic strategies against pathogenic infection, allergies, malignant neoplasms and autoimmunity. This review summarizes the therapeutic applications of nucleic acids or nucleic acid analogues through the modulation of TLR signaling pathways.
The Rationale for Prostaglandin E1 in Erectile Failure: A Survey of Worldwide Experience (1996)

For self-injection therapy, PGE1 presently represents the most efficacious and safest drug. Ongoing trials with topical and especially intraurethral PGE1 are promising and may offer less invasive therapies in the near future.
Photochemistry of ommochromes and related compounds (1988)

Abstract The photochemistry of some synthetic ommochromes, the 1‐methoxy‐11‐(β‐aspartoyl‐acetyl‐methyl ester)‐5 H ‐pyrido[3,2‐ a ]phenoxazin‐5‐one ( 2 ), the 1‐methyl‐1‐(1′‐[1′[11‐(β‐aspartoyl‐methyl ester‐imino)]ethenyl)‐ketal‐1 H ,5 H ‐pyrido[3,2‐ a ]phenoxazin‐5‐one ( 3 ) and the 1,5‐dimethoxy‐11‐(β‐aspartoyl‐ N ‐acetyl‐methyl ester)‐pyrido[3,2‐ a ]phenoxazine ( 4 ), obtained from the oxidation of the 3‐hydroxykynurenine ( 1 ), has been examined. In an acidic methanol solution of 2 , a reversible solvent photoaddition was observed, associated with a yellow‐red bathochromic shift. The mixture, stored in the dark, quantitatively records the starting absorption spectrum. In an acidic enviroment, 3 and 4 , affording 2 , show the same photochemical behaviour. A plausible mechanism, for explanation of the process is suggested.
Direct activation of antigen-presenting cells is required for CD8 + T-cell priming and tumor vaccination (2011)

Successful priming of adaptive immune responses is crucially dependent on innate activation signals that convert resting antigen-presenting cells (APCs) into immunogenic ones. APCs expressing the relevant innate pattern recognition receptors can be directly activated by pathogen-associated molecular patterns (PAMPs) to become competent to prime T-cell responses. Alternatively, it has been suggested that APCs could be activated indirectly by proinflammatory mediators synthesized by PAMP-exposed cells. However, data obtained with CD4(+) T cells suggest that inflammatory signals often cannot substitute for direct pattern recognition in APC activation for the priming of T helper responses. To test whether the same is true for CD8(+) T cells, we studied cytotoxic T lymphocyte development in vitro and in mixed chimeric mice in which coexisting APCs can either present a preprocessed model antigen or directly recognize a given PAMP, but not both. We show that indirectly activated APCs promote antigen-specific proliferation of naïve CD8(+) T cells but fail to support their survival and cytotoxic T lymphocyte differentiation. Furthermore, CD8(+) T cells primed by indirectly activated APCs are unable to reject tumors. Thus, inflammation cannot substitute for direct recognition of single PAMPs in CD8(+) T-cell priming. These findings have important practical implications for vaccine design, indicating that adjuvants must be judiciously chosen to trigger the relevant pattern recognition receptors in APCs.