gebhart/patrepeval huggingface dataset:
Site-specific glycoproteomics confirms that protein structure dictates formation of N-glycan type, core fucosylation and branching (2012)

Growing evidence indicates that the individualized and highly reproducible N-glycan repertoires on each protein glycosylation site modulate function. Relationships between protein structures and the resulting N-glycoforms have previously been observed, but remain to be quantitatively confirmed and examined in detail to define the responsible mechanisms in the conserved mammalian glycosylation machinery. Here, we investigate this relationship by manually extracting and analyzing quantitative and qualitative site-specific glycoprofiling data from 117 research papers. Specifically, N-glycan structural motifs were correlated with the structure of the protein carriers, focusing on the solvent accessibility of the individual glycosylation sites and the physicochemical properties of the surrounding polypeptide chains. In total, 474 glycosylation sites from 169 mammalian N-glycoproteins originating from different tissues/body fluids were investigated. It was confirmed statistically that the N-glycan type, degree of core fucosylation and branching are strongly influenced by the glycosylation site accessibility. For these three N-glycan features, glycosylation sites carrying highly processed glycans were significantly more solvent-accessible than those carrying less processed counterparts. The glycosylation site accessibilities could be linked to molecular signatures at the primary and secondary protein levels, most notably to the glycoprotein size and the proportion of glycosylation sites located in accessible β-turns. In addition, the subcellular location of the glycoproteins influenced the formation of the N-glycan structures. These data confirm that protein structures dictate site-specific formation of several features of N-glycan structures by affecting the biosynthetic pathway. Mammals have, as such, evolved mechanisms enabling proteins to influence the N-glycans they present to the extracellular environment.
Metabolic engineering of Escherichia coli for the production of putrescine: A four carbon diamine (2009)

A four carbon linear chain diamine, putrescine (1,4-diaminobutane), is an important platform chemical having a wide range of applications in chemical industry. Biotechnological production of putrescine from renewable feedstock is a promising alternative to the chemical synthesis that originates from non-renewable petroleum. Here we report development of a metabolically engineered strain of Escherichia coli that produces putrescine at high titer in glucose mineral salts medium. First, a base strain was constructed by inactivating the putrescine degradation and utilization pathways, and deleting the ornithine carbamoyltransferase chain I gene argI to make more precursors available for putrescine synthesis. Next, ornithine decarboxylase, which converts ornithine to putrescine, was amplified by a combination of plasmid-based and chromosome-based overexpression of the coding genes under the strong tac or trc promoter. Furthermore, the ornithine biosynthetic genes (argC-E) were overexpressed from the trc promoter, which replaced the native promoter in the genome, to increase the ornithine pool. Finally, strain performance was further improved by the deletion of the stress responsive RNA polymerase sigma factor RpoS, a well-known global transcription regulator that controls the expression of ca. 10% of the E. coli genes. The final engineered E. coli strain was able to produce 1.68 g L(-1) of putrescine with a yield of 0.168 g g(-1) glucose. Furthermore, high cell density cultivation allowed production of 24.2 g L(-1) of putrescine with a productivity of 0.75 g L(-1) h(-1). The strategy reported here should be useful for the bio-based production of putrescine from renewable resources, and also for the development of strains capable of producing other diamines, which are important as nitrogen-containing platform chemicals.
Angola's Current Economic Prospects: Oil Curse or Blessing? (2009)

Cervical spinal epidural hematoma is an infrequent entity that usually requires emergency decompressive therapy because of rapid neurologic dysfunction. We present the case of a 34-year-old man who presented to the emergency department with minimal symptomatology after a stab wound to the neck. A computed tomography myelogram of the cervical spine revealed a cervical spinal epidural hematoma. This case illustrates an unusual presentation as well as etiology of cervical spinal epidural hematoma.
A CD4/Foxp3/OX40 triple immunofluorescence assay determines association between T cell immune subsets and outcome in colorectal cancer (2014)

Meeting abstracts Increased numbers of OX40+ T cells in the tumor microenvironment of colorectal cancer (CRC) patients have been associated with improved outcome. However, the OX40+ T cell population is heterogeneous and includes, among others, CD4+Foxp3+ regulatory T cells (Treg) as well as CD4+
Antigenic Mapping of the Surface Proteins of Infectious Hepatitis B Virus Particles (1987)

To identify further the surface proteins of the native virus, hepatitis B virus (HBV) particles purified from HBe antigen (Ag)-positive human sera were used as immunogens to produce murine monoclonal antibody (MAb)-secreting hybridomas. The specific binding of antibodies to the HBV envelope (env) proteins was determined in indirect radioimmunoassay and by Western blot analysis. Six MAbs directed against major hepatitis B surface antigen (HBsAg) recognized conformational epitopes on S proteins (P24s/GP27s). Three preS2-specific MAbs reacted with the middle env proteins (GP33s/GP36s) in the 22 nm HBsAg spherical particles. One MAb, F222, was found to react specifically with the two very large (VL) HBV surface proteins with Mr 54K and 66K. The epitope recognized by F222 was located on the protruding N terminus which, in the assembled virus particles, was readily split off by trypsin or V8 protease treatment. The presence of these VL proteins appeared to correspond to the presence of the large env proteins (P39s/GP42s). The data described here indicate that F222 probably recognized an assembled topographic site which could be involved in virus entry into hepatocytes. Moreover, our results suggest that the preS-coded part of the HBV env proteins, which is sensitive to proteases in vitro, could be unstable in vivo and stabilized by immunoglobulins.
Biometric cryptosystems: issues and challenges (2004)

In traditional cryptosystems, user authentication is based on possession of secret keys; the method falls apart if the keys are not kept secret (i.e., shared with non-legitimate users). Further, keys can be forgotten, lost, or stolen and, thus, cannot provide non-repudiation. Current authentication systems based on physiological and behavioral characteristics of persons (known as biometrics), such as fingerprints, inherently provide solutions to many of these problems and may replace the authentication component of traditional cryptosystems. We present various methods that monolithically bind a cryptographic key with the biometric template of a user stored in the database in such a way that the key cannot be revealed without a successful biometric authentication. We assess the performance of one of these biometric key binding/generation algorithms using the fingerprint biometric. We illustrate the challenges involved in biometric key generation primarily due to drastic acquisition variations in the representation of a biometric identifier and the imperfect nature of biometric feature extraction and matching algorithms. We elaborate on the suitability of these algorithms for digital rights management systems.
Reversible Inhibition of Protein Splicing by Zinc Ion (2001)

Protein splicing involves the self-catalyzed excision of a protein-splicing element, the intein, from flanking polypeptides, the exteins, which are concomitantly joined by a peptide bond. Taking advantage of recently developed in vitro systems in which protein splicing occurs in trans to assay for protein-splicing inhibitors, we discovered that low concentrations of Zn(2+) inhibited splicing mediated both by the RecA intein from Mycobacterium tuberculosis and by the naturally split DnaE intein from Synechocystis sp. PCC6803. Inhibition by Zn(2+) was also observed with a cis-splicing system involving the RecA intein. In all experimental systems used, inhibition by Zn(2+) could be completely reversed by the addition of EDTA. Zinc ion also inhibited hydroxylamine-dependent N-terminal cleavage of the RecA intein. All other divalent transition metal ions tested were less effective as inhibitors than Zn(2+). The reversible inhibition by Zn(2+) should be useful in studies of the mechanism of protein splicing and allow structural studies of unmodified protein-splicing precursors.
2013년 봄 : 복지와 노동(권력): “권력자원접근”의 이론적 위상과 한국적 함의 (2013)

이 글은 복지국가 형성/발전의 주체와 관련하여 이른바 권력자원접근과 그것을 둘러싼 최근의 이론적 논의들을 돌아보고, 권력자원접근의 유효성과 한국적 실정과의 관련성을 살핀다. 이러한 관심은, 부분적으로는, 작금 한국에 융성하는 복지담론들과 이론적 시도들이 국가복지의 규범적 당위성 아니면 복지정책들에 대한 미시적 분석에 많이 경사돼 있어서 막상 복지국가의 형성에 관련한 주체의 문제를 상대적으로 소홀히 취급하고 있다는, 다분히 실천적인 인식에서 비롯되었다. 노동은 하나는 독립변수로서, 다른 하나는 종속변수로서 복지국가에 관여한다. 전자는 노동(계급)의 권력이 복지국가의 발전에 작용하는 맥락에, 후자는 형성된 복지국가가 노동의 탈상품화에 기여하는 정도에 연결된다. 이 논문은 전자, 곧 복지국가 발전의 주체의 문제에 주목한 글이다. 탈상품화 곧 복지국가가 노동을 포용하는 방식과 수준은 다양할지라도, 사회경제적 약자들이 인생행로에서 부딪치는 리스크들에 대한 노출 정도와 거기에 대응하는 역량―대체로 이는 복지국가 지출의 총량적 수준이나 복지프로그램들의 소득대체율 등으로 표출된다―은 넓은 의미의 노동계급의 권력자원에 총체적으로 의존한다는 것이 이 글의 기본가정이다. 이런 가정은 ``노동→복지국가→노동``의 고리, 곧 복지국가의 형성세력과 수혜자 집단의 이해관계가 크게 다른 것이 아니라는 전제에 서 있다. 사회적 리스크의 편차가 계급관련 집단행동의 잠재력을 높인다는 것인데, 가령 고용관계는 계급적 분화를 낳고 노동계급은 삶의 역정에서 리스크 노출의 정도가 크고 그것을 극복할 자원은 취약하기 때문에 노조와 노동자정당을 통해 권력자원을 증대시키고 리스크 부담(비용)을 줄이려한다.
Enzymic Characterization of the Target for Isoniazid in Mycobacterium tuberculosis (1995)

The inhA gene has been recently shown to encode a common protein target for isoniazid and ethionamide action in Mycobacterium tuberculosis. In this paper, we demonstrate that the M. tuberculosis InhA protein catalyzes the NADH-specific reduction of 2-trans-enoyl-ACP, essential for fatty acid elongation. This enzyme preferentially reduces long-chain substrates (12-24 carbons), consistent with its involvement in mycolic acid biosynthesis. Steady-state kinetic studies showed that the two substrates bind to InhA via a sequential kinetic mechanism, with the preferred ordered addition of NADH and the enoyl substrate. The chemical mechanism involves stereospecific hydride transfer of the 4S hydrogen of NADH to the C3 position of the 2-trans-enoyl substrate, followed by protonation at C2 of an enzyme-stabilized enolate intermediate. Kinetic and microcalorimetric analysis demonstrates that the binding of NADH to the S94A mutant InhA, known to confer resistance to both isoniazid and ethionamide, is altered. This difference can account for the isoniazid-resistance phenotype, with the formation of a binary InhA-NADH complex required for drug binding. Isoniazid binding to either the wild-type or S94A mutant InhA could not be detected by titration microcalorimetry, suggesting that this compound is a prodrug, which must be converted to its active form.
A mixed digital-analog 16 b microcontroller with 0.5 Mb flash memory, on-chip power supply, physical network interface, and 40 V I/O for automotive single-chip mechatronics (2002)

Automotive electronics are the driving force for real-time controller area networks (CAN) with up to 100 nodes in a future high-end vehicle. The mixed mechanical-electronic (mechatronic) control units in such a network require single-chip microsystems to achieve reliable cost-effective systems integration with a minimum number of components and interconnections. The mixed digital-analog microcontroller meets these mechatronic requirements. In addition to a complex 16 b flash programmable microcontroller, it includes a set of robust analog I/O peripherals such as voltage regulator, bus interface, and sensor interface with 40 V break-down, so that no external interface ICs are required.
Action Spectrum for the Photoperiodic Control of Floral Initiation of Short-Day Plants (1946)

1. The purposes of this investigation were to obtain quantitative data on the photoreactions that prevent flowering of short-day plants, from which an action spectrum relating wave length to photoperiodic effectiveness of light could be derived, and to draw such inferences concerning the nature of the photoreactions as the action spectrum would permit. 2. Experiments designed to give the action spectrum made use of a specially designed prism spectrograph having a dispersion of 15 A. per cm. at 5000 A. At this wave length and with an effective slit width of 100 A. the energy was about 3000 ergs per sq. cm. per second with the slit illuminated by a carbon arc operated at 12 kw. input. 3. Plants investigated were soybean, Soja max (L.) Piper var. Biloxi, and cocklebur, Xanthium saccharatum Wallr. To facilitate irradiation, the foliar surface of the plants of each species at the beginning of an experiment was reduced to a single leaflet or leaf, respectively. 4. The experimental treatment was based on the fact that flowering of short-day plants receiving short photoperiods can be prevented by interrupting each of the accompanying long dark periods at or near the middle with a brief period of irradiation. In these experiments minimal energies required to prevent floral initiation were determined for many narrow regions of the spectrum. 5. The reciprocity law was tested and found to hold for the factors of time and intensity within the ranges used for dark-period interruption. Flowering response of both soybean and cocklebur depends on the total radiant energy used to interrupt the dark period. 6. Minimal energies necessary to prevent flowering depend upon the number of hours of darkness elapsing before the plants are irradiated but are constant over a 2-hour period beginning 30 minutes before the middle of the dark period. 7. Action spectra for soybean and cocklebur are similar in several respects. The limit of effectiveness of radiation for preventing flowering of both plants is near 7200 A., at the red end of the spectrum. Maximum effectiveness for both plants occurs over a broad region extending from about 6000 to 6800 A. A minimum of effectiveness of radiation for both plants occurs in the region of 4800 A., and effectiveness increases again at shorter wave lengths in the visible portion of the spectrum. 8. Ratios of energies required to prevent flowering in the regions of maximum and of minimum effectiveness were different for the two plants, being about 1:200 for cocklebur and 1:60 for soybean. 9. The possibility that chlorophyll may be the effective pigment in the photoperiodic reaction is examined.
The Double-Blind Variable Placebo Lead-in Period: Results From Two Antidepressant Clinical Trials (2001)

The 1-week single-blind placebo lead-in has long been a standard in double-blind psychopharmacology clinical trials. Although a lead-in period is often necessary (e.g., to receive laboratory results before randomization), some authors have demonstrated that the standard single-blind placebo lead-in's performance was similar to having a lead-in in which placebo was not administered. The single-blind placebo lead-in did not decrease postrandomization placebo response, nor did it increase drug-placebo differences. To eliminate a higher percentage of placebo responders before randomization and to reduce potential biases in baseline ratings, the authors designed and implemented two depression studies with a double-blind variable placebo lead-in period. In these designs, both the patients and personnel at the investigative sites were blinded to the length of the placebo lead-in period and the start of the active treatment period. Approximately 28% of the patients in the double-blind placebo lead-in studies met criteria to be placebo lead-in responders, as compared with fewer than 10% from two single-blind placebo lead-in studies conducted in a similar time frame. Although all patients continued in the study (including placebo lead-in responders), the primary efficacy analysis prospectively excluded double-blind placebo lead-in responders. Analysis of postrandomization changes revealed that double-blind placebo lead-in responders, even when continuing to receive placebo treatment, maintained their response. At the study endpoint, these placebo lead-in responders had significantly lower severity scores than their counterparts who were not lead-in responders. The prospective removal of lead-in responders thus resulted in an increase in mean endpoint placebo group severity scores. This resulted in an increased drug-placebo treatment difference in one of the two studies but had no effect on the treatment difference in the other study.
Neurotrophic factors in sponal pain transmission (2006)

Het doel van dit proefschrift was de betrokkenheid van Glial Cell Line-Derived Neurotrophic Factor \n(GDNF) bij spinale pijntransmissie te bestuderen. In Hoofdstuk 1 worden enkele recente ontwikkelen \nbetreffende de organisatie van het nociceptieve systeem besproken, gevolgd door een beschrijving van \nde betrokkenheid van neurotrofe factoren in sensibele transmissie. Dit is de achtergrondinformatie die \nnodig is om de bevindingen in de volgende hoofdstukken te kunnen interpreteren.
Evaluation of a mass screening program for stomach cancer with a case‐control study design (1986)

In order to evaluate the effectiveness of a mass screening program for stomach cancer, a case-control study was conducted in Nose town in Osaka, Japan. The case series consisted of all deaths from stomach cancer during the period 1969-1981 (54 in males and 37 in females). For each case, 3 controls of the same sex and from the same precinct as the case, and born within 5 years of the case birth-year, were selected at random from Nose town residents alive at the date of death of the relevant case. We then investigated whether each case and corresponding controls had ever had screening tests before the date of diagnosis of the case. From the matched analysis of the distribution of screening in case-control combination, the odds ratio of screened vs. unscreened among those who died from stomach cancer compared to those who did not was calculated as 0.595 (90% confidence interval: 0.338-1.045) among males and 0.382 (0.185-0.785) among females. When the screening tests conducted within 12 months of diagnosis were ignored on the presumption that they were symptom-related, the odds ratio was calculated as 0.519 (0.297-0.905) among males and 0.486 (0.239-0.986) among females. These data strongly suggest that the mass screening program is effective in reducing stomach cancer mortality.
Neural pathways involved in sacral neuromodulation of reflex bladder activity in cats (2013)

This study examined the mechanisms underlying the effects of sacral neuromodulation on reflex bladder activity in chloralose-anesthetized cats. Bladder activity was recorded during cystometrograms (CMGs) or under isovolumetric conditions. An S1-S3 dorsal (DRT) or ventral root (VRT) was electrically stimulated at a range of frequencies (1-30 Hz) and at intensities relative to threshold (0.25-2T) for evoking anal/toe twitches. Stimulation of DRTs but not VRTs at 1T intensity and frequencies of 1-30 Hz inhibited isovolumetric rhythmic bladder contractions. A 5-Hz DRT stimulation during CMGs was optimal for increasing (P < 0.05) bladder capacity (BC), but stimulation at 15 and 30 Hz was ineffective. Stimulation of the S1 DRT was more effective (increases BC to 144% and 164% of control at 1T and 2T, respectively) than S2 DRT stimulation (increases BC to 132% and 150% of control). Bilateral transection of the hypogastric or pudendal nerves did not change the inhibitory effect induced by S1 DRT stimulation. Repeated stimulation of S1 and S2 DRTs during multiple CMGs elicited a significant (P < 0.05) increase in BC (to 155 ± 11% of control) that persisted after termination of the stimulation. These results in cats suggest that the inhibition of reflex bladder activity by sacral neuromodulation occurs primarily in the central nervous system by inhibiting the ascending or descending pathways of the spinobulbospinal micturition reflex.
Defective Suppressor Function of Human CD4+ CD25+ Regulatory T Cells in Autoimmune Polyglandular Syndrome Type II (2004)

In autoimmune polyglandular syndromes (APS), several organ-specific autoimmune diseases are clustered. Although APS type I is caused by loss of central tolerance, the etiology of APS type II (APS-II) is currently unknown. However, in several murine models, depletion of CD4(+) CD25(+) regulatory T cells (T(regs)) causes a syndrome resembling human APS-II with multiple endocrinopathies. Therefore, we hypothesized that loss of active suppression in the periphery could be a hallmark of this syndrome. T(regs) from peripheral blood of APS-II, control patients with single autoimmune endocrinopathies, and normal healthy donors showed no differences in quantity (except for patients with isolated autoimmune diseases), in functionally important surface markers, or in apoptosis induced by growth factor withdrawal. Strikingly, APS-II T(regs) were defective in their suppressive capacity. The defect was persistent and not due to responder cell resistance. These data provide novel insights into the pathogenesis of APS-II and possibly human autoimmunity in general.
SPASYN-an electromagnetic relative position and orientation tracking system (1980)

Two relatively remote independent body coordinate frames are related in both position and orientation (six degrees of freedom) using precise electromagnetic field measurements. Antenna triads are fixed in each body frame. Variously polarized excitations in one body are correlated with signals detected in the remote body. Near-field and far-field processing strategies are presented with applications.
Short-term Prognosis After Emergency Department Diagnosis of TIA (2000)

Our results indicate that the short-term risk of stroke and other adverse events among patients who present to an ED with a TIA is substantial. Characteristics of the patient and the TIA may be useful for identifying patients who may benefit from expeditious evaluation and treatment.
Cleavage site determinants min the mammalian polydenylation signal (1995)

Using a series of position and nucleotide variants of the SV40 late polyadenylation signal we have demonstrated that three sequence elements determine the precise site of 3-end cleavage in mammalian pre-mRNAs: an upstream AAUAAA element, a down-stream U-rich element consisting of five nucleotides, at least four of which are uridine, and a nucleotide preference at the site of cleavage in the order A > U > C >> G. Cleavage occurs no closer than 11 bases, but no further than 23 bases from the AAUAAA element. The downstream U-rich element is usually located 10-30 bases from the cleavage site. The relative position of the AAUAAA and the U-rich elements define the approximate region within a 13 base domain in which cleavage will occur. The exact position of cleavage is then determined by the local nucleotide sequence in the order of preference noted above. This model accounts for nearly three quarters of polyadenylation signals surveyed and is consistent with previous experimental observations.
Defective Cholesterol Biosynthesis Associated with the Smith-Lemli-Opitz Syndrome (1994)

The combination of abnormally low plasma cholesterol levels and a high concentration of the cholesterol precursor 7-dehydrocholesterol points to a major block in cholesterol biosynthesis at the step in which the C-7(8) double bond of 7-dehydrocholesterol is reduced, forming cholesterol. The block may be sufficient to deprive an embryo or fetus of cholesterol and prevent normal development, whereas the incorporation of 7-dehydrocholesterol into all membranes may interfere with proper membrane function.