gebhart/patrepeval huggingface dataset:
Analysis of Phosphorylated Sphingolipid Long-Chain Bases Reveals Potential Roles in Heat Stress and Growth Control in Saccharomyces (1999)

Sphingolipid long-chain bases and their phosphorylated derivatives, for example, sphingosine-1-phosphate in mammals, have been implicated as signaling molecules. The possibility that Saccharomyces cerevisiae cells also use long-chain-base phosphates to regulate cellular processes has only recently begun to be examined. Here we present a simple and sensitive procedure for analyzing and quantifying long-chain-base phosphates in S. cerevisiae cells. Our data show for the first time that phytosphingosine-1-phosphate (PHS-1-P) is present at a low but detectable level in cells grown on a fermentable carbon source at 25 degreesC, while dihydrosphingosine-1-phosphate (DHS-1-P) is only barely detectable. Shifting cells to 37 degreesC causes transient eight- and fivefold increases in levels of PHS-1-P and DHS-1-P, respectively, which peak after about 10 min. The amounts of both compounds return to the unstressed levels by 20 min after the temperature shift. These data are consistent with PHS-1-P and DHS-1-P being signaling molecules. Cells unable to break down long-chain-base phosphates, due to deletion of DPL1 and LCB3, show a 500-fold increase in PHS-1-P and DHS-1-P levels, grow slowly, and survive a 44 degreesC heat stress 10-fold better than parental cells. These and other data for dpl1 or lcb3 single-mutant strains suggest that DHS-1-P and/or PHS-1-P act as signals for resistance to heat stress. Our procedure should expedite experiments to determine how the synthesis and breakdown of these compounds is regulated and how the compounds mediate resistance to elevated temperature.
Pneumococci causing invasive disease in New Zealand, 1987-94: serogroup and serotype coverage and antibiotic resistances. (1996)

The serogroups and serotypes found most frequently associated with pneumococcal disease, and antibiotic resistance, were consistent with those described overseas. Continuing surveillance of antibiotic resistances and serotypes of pneumococci causing invasive disease is recommended.
Formation ofStreptococcus pneumoniaeNon-Phase-Variable Colony Variants Is Due to Increased Mutation Frequency Present under Biofilm Growth Conditions (2008)

In this report, we show that biofilm formation by Streptococcus pneumoniae serotype 19 gives rise to variants (the small mucoid variant [SMV] and the acapsular small-colony variant [SCV]) differing in capsule production, attachment, and biofilm formation compared to wild-type strains. All biofilm-derived variants harbored SNPs in cps19F. SCVs reverted to SMV, but no reversion to the wild-type phenotype was noted, indicating that these variants were distinct from opaque- and transparent-phase variants. The SCV-SMV reversion frequency was dependent on growth conditions and treatment with tetracycline. Increased reversion rates were coincident with antibiotic treatment, implicating oxidative stress as a trigger for the SCV-SMV switch. We, therefore, evaluated the role played by hydrogen peroxide, the oxidizing chemical, in the reversion and emergence of variants. Biofilms of S. pneumoniae TIGR4-DeltaspxB, defective in hydrogen peroxide production, showed a significant reduction in variant formation. Similarly, supplementing the medium with catalase or sodium thiosulfate yielded a significant reduction in variants formed by wild-type biofilms. Resistance to rifampin, an indicator for mutation frequency, was found to increase approximately 55-fold in biofilms compared to planktonic cells for each of the three wild-type strains examined. In contrast, TIGR4-DeltaspxB grown as a biofilm showed no increase in rifampin resistance compared to the same cells grown planktonically. Furthermore, addition of 2.5 and 10 mM hydrogen peroxide to planktonic cells resulted in a 12- and 160-fold increase in mutation frequency, respectively, and gave rise to variants similar in appearance, biofilm-related phenotypes, and distribution of biofilm-derived variants. The results suggest that hydrogen peroxide and environmental conditions specific to biofilms are responsible for the development of non-phase-variable colony variants.
MODL-01. Targeting replication stress in pediatric brain tumors (2022)

Abstract Previously, we have found that Embryonal Tumors with Multilayered Rosettes (ETMR) tumor cells harboring high levels of R-loops, a potential marker for replication stress and genomic instability, are vulnerable to a combination of topoisomerase and PARP inhibitors. To follow up on this, we investigated whether other pediatric brain tumor types with high levels of R-loops, such as MYC-amplified Group 3 medulloblastoma (MB) and ZFTA-fusion positive ependymoma, are also sensitive to these inhibitors. First, we performed in vitro drug screens using HD-MB03, a Group 3 MB cell line, and the ETMR cell line BT183, and in both screens PARP inhibitors were identified as the most synergistic combination partners for the topoisomerase inhibitor Irinotecan, respectively the active metabolite SN-38. Normal Astrocytes were not sensitive to these combinations. Secondly, we performed in vivo studies using patient-derived xenograft (PDX) models injected subcutaneously or intracranially into NSG mice, and treated with the PARP inhibitor Pamiparib, Irinotecan or a combination of both. For a MYC-amplified Group 3 MB and a ZFTA-fusion positive Ependymoma model, both injected intracranially, treatment with Irinotecan or the combination led to a significant survival benefit and inhibition of tumor growth including transient tumor shrinkage, but addition of Pamiparib did not add any further benefit in vivo, even though intratumoral PARP was inhibited by at least 80%. In contrast, in the subcutaneously injected ETMR model, the combination treatment with Irinotecan and Pamiparib led to a synergistic effect and complete regression of the tumors. Further refinements of the treatment strategy as dose adaptations and the use of a pegylated version of SN-38 (PLX038A) did also not induce a synergistic effect of the drugs for the intracranial tumors. Additional in vivo studies to evaluate the differences in efficacy and whether these are tumor specific or due to incomplete brain penetrance of the drugs are ongoing.
Hollow polymer particles that are pH-responsive and redox sensitive: two simple steps to triggered particle swelling, gelation and disassembly (2010)

A new, simple, two-step method is introduced for preparing hollow particles that are both pH-responsive and redox sensitive. Hollow poly(methyl methacrylate-co-methacrylic acid) particles swell at moderate pH values, form gels in concentrated dispersions and can be disassembled by adding reducing agents.
Chemical Inhibition of PTEN‐Induced Kinase 1 (PINK1) Degradation Confers Neuroprotection in Culture Models of Parkinson’s Disease (2020)

PTEN‐induced kinase 1 (PINK1) loss of function is linked to familial recessive Parkinson’s disease and, more recently, sporadic Alzheimer’s disease. After mitochondrial processing and release, PINK1 is rapidly degraded by the proteasome. Objective We hypothesized that stabilization of PINK1 by interfering with binding to its SCF ubiquitin ligase complex would elevate PINK1 expression levels and confer neuroprotection. Methods &amp; Results After identifying an F‐box protein that interacted with PINK1 and regulated PINK1 expression levels, we used computational binding simulations to screen compounds likely to interfere with this interaction. We identified a small molecule that stabilized PINK1 expression and reduced both cell death and dendritic retraction in several models of Parkinsonian injury in primary cortical neurons and patient‐derived cells. Conclusions Our identification of an F‐box protein‐targeted small molecule antagonist capable of elevating endogenous PINK1 levels sets the stage for additional target validation for the potential treatment of neurodegenerative diseases and other disorders characterized by mitochondrial dysfunction. Support or Funding Information Grant support: NIH grants AG026389, NS101628 (co‐funded by NINDS/NIA) and NS065789 (C.T.C.), HL096376, HL097376, HL098174, HL081784, P01 HL114453 and Merit Review Award from the United States Department of Veterans Affairs (R. K. M.), HL139860 and HL133184 (B.B.C.), HL142777 and AHA 16SDG27650008 (Y.L.). The content is solely the responsibility of the authors and does not represent the official views of the National Institutes of Health.
Association between the glutathione S‐transferase M1 gene deletion and female methamphetamine abusers (2003)

Several lines of evidence suggest that increased generation of auto-oxidized dopamine (DA) o-quinone is associated with the neurotoxicity of methamphetamine (MAP) in the brain, and that, as a cellular defenses against DA-derived quinines, glutathione S-transferase (GST) detoxifies auto-oxidized DA o-quinone in the brain. Glutathione S-transferase M1 (GSTM1) of the mu-class of GSTs catalyzes reaction between glutathione and catecholamine o-quinones under physiological conditions. This study was undertaken to investigate the role of the GSTM1 gene deletion polymorphism in the neuropathology of MAP abuse. One hundred fifty-seven MAP abusers and 200 healthy comparison subjects were tested for a genetic polymorphism of GSTM1. The difference in the frequency of deletion (D)/non-deletion (N) alleles between the female abusers and female controls was close to statistical significance (P = 0.071), although there was no statistical difference (P = 0.651) between male abusers and male controls. Furthermore, the number of female abusers with deletion alleles was significantly (P = 0.007, odds ratio: 2.77, 95% CI 1.30-5.89) higher than that of male abusers with deletion alleles. These findings suggest that GSTM1 gene deletion may contribute to a vulnerability to MAP abuse in female subjects, but not in male subjects.
ISCHEMIC CEREBROVASCULAR COMPLICATIONS OF HAEMOPHILUS INFLUENZAE MENINGITIS (1983)

Department of Neurology, Tulane University School of Medicine, 1415 Tulane Avenue, New Orleans, LA 70112
Suppressing the Surface Field During Transcranial Magnetic Stimulation (2006)

Transcranial magnetic stimulation (TMS) is used commonly as both a diagnostic tool and as an alternative to electric shock therapy for the treatment of clinical depression. Among the clinical issues encountered in its use is the mitigation of accompanying pain. The objective becomes one of minimizing the induced surface field while still achieving the target field objective. Three techniques discussed for realizing this end are 1) placing a conducting shield over a portion of the central target region, 2) using supplementary coils of opposite polarity in tandem with the primary field, and 3) opening the core angle to distribute the field. Option (3) shows the greatest promise for reducing the ratio of the maximum surface field to the induced target field.
Screening pharmaceutical preparations containing extracts of turmeric rhizome, artichoke leaf, devil's claw root and garlic or salmon oil for antioxidant capacity (2003)

Pharmaceutical preparations derived from natural sources such as vegetables often contain compounds that contribute to the antioxidant defence system and apparently play a role in the protection against degenerative diseases. In the present study, commercial preparations containing extracts of turmeric, artichoke, devil's claw and garlic or salmon oil were investigated. The products were divided into fractions of different polarity, and their antioxidant activity was determined using the Trolox equivalent antioxidant capacity (TEAC) assay. This test is based on the efficacy of the test material to scavenge 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) derived radicals. Total phenols were determined in all fractions as well as specific carotenoids in the most lipophilic fraction to assess their contribution to the antioxidant activity. For comparison, the radical scavenging effect of selected constituents of the extracts such as curcumin, luteolin, kaempferol, chlorogenic acid, harpagoside, beta-carotene and alpha-tocopherol was investigated and compared with that of Trolox. Curcumin, luteolin, kaempferol, chlorogenic acid and beta-carotene showed an antioxidant activity superior to Trolox in the TEAC assay; harpagoside was barely active. All fractions of the turmeric extract preparation exhibited pronounced antioxidant activity, which was assigned to the presence of curcumin and other polyphenols. The antioxidant activity corresponding to the artichoke leaf extract was higher in the aqueous fractions than in the lipophilic fractions. Similarly, devil's claw extract was particularly rich in water-soluble antioxidants. Harpagoside, a major compound in devil's claw, did not contribute significantly to its antioxidant activity. The antioxidant capacity of the garlic preparation was poor in the TEAC assay. That of salmon oil was mainly attributed to vitamin E, which is added to the product for stabilization. In all test preparations, the antioxidant activity was significantly correlated with the content of total phenolic compounds.
ChemInform Abstract: DARST. UND RK. EINES BIS‐(PENTAFLUORPHENYL)‐KOBALT‐KOMPLEXES (1972)

Abstract Bei Zugabe von Pentafluorphenylmagnesiumbromid (II) zu gelöstem Kobalt(II)‐bromid (I) bildet sich ein Produkt, das wie Bis‐(pentafluorphenyl)‐kobalt (III) reagiert.
Evaluation of an Injectable Biphasic Calcium Sulfate/Hydroxyapatite Cement for the Augmentation of Fenestrated Pedicle Screws in Osteoporotic Vertebrae: A Biomechanical Cadaver Study (2022)

Cement augmentation of pedicle screws is one of the most promising approaches to enhance the anchoring of screws in the osteoporotic spine. To date, there is no ideal cement for pedicle screw augmentation. The purpose of this study was to investigate whether an injectable, bioactive, and degradable calcium sulfate/hydroxyapatite (CaS/HA) cement could increase the maximum pull-out force of pedicle screws in osteoporotic vertebrae. Herein, 17 osteoporotic thoracic and lumbar vertebrae were obtained from a single fresh-frozen human cadaver and instrumented with fenestrated pedicle screws. The right screw in each vertebra was augmented with CaS/HA cement and the un-augmented left side served as a paired control. The cement distribution, interdigitation ability, and cement leakage were evaluated using radiographs. Furthermore, pull-out testing was used to evaluate the immediate mechanical effect of CaS/HA augmentation on the pedicle screws. The CaS/HA cement presented good distribution and interdigitation ability without leakage into the spinal canal. Augmentation significantly enhanced the maximum pull-out force of the pedicle screw in which the augmented side was 39.0% higher than the pedicle-screw-alone side. Therefore, the novel biodegradable biphasic CaS/HA cement could be a promising material for pedicle screw augmentation in the osteoporotic spine.
Targeted expression of a lumican transgene rescues corneal deficiencies in lumican-null mice. (2007)

Together these data suggest that despite the low keratocan promoter activity driving the transgene in Lum(-/-) cornea, transgenic lumican expression was sufficient to partially rescue corneal phenotypic deficiencies.
Hexamethylenetetramine-Ionic Liquids Catalyzed Baylis-Hillman Reactions (2006)

In the present paper it is described the use of hexamethylenetetramine combined to the use of bmim+ type ionic liquids as cheap, environmentally friendly and efficient catalytic systems for Baylis- Hillman reactions between aromatic aldehydes and acrylonitrile or methyl acrylate. The Baylis-Hillman adducts were obtained in moderate to good yields (50-85%), in short reaction times. The ionic liquids can be recycled. Keywords: BmimPF6, bmimBF4, hexamethylenetetramine, non innocent, catalysis, green chemistry
Primary Malignant Melanoma of the Esophagus (1975)

A rare case of primary malignant melanoma developing in the esophagus was described.A 45 year old man was admitted to our clinic on Apr. 5, 1974, complaining ofoccasional feeling of dysphagia for several months. General examination was negativefor melanotic lesions, including examinations of the skin, anus, both eyes and upperrespiratory tract. X-ray examinations disclosed a polypoid and multilobulated lesion atthe middle third of the esophagus.Selective accumulation of RI in this lesion was also demonstrated by 67 Ga-citratescintigraphy. Esophagoscopy revealed a dark-bluish mass protruding circumferentiallytoward the lumen of the esophagus; its surface was relatively smooth, soft, partiallyeroded and easily bled on instrumentation.Histologic examination of a biopsy of this lesion showed a diffuse tumor growth underthe epithelial layer of the esophagus. The tumor cells formed epitheloid clusters orsheets of streaming arrays and had eosinophilic cytoplasm with or without dark-brownpigment granules which were readily removed with hydrogen peroxide and stained withsilver but did not contain iron.All the above mentioned data strongly indicated that the tumor was a primary malignantmelanoma originating in the esophagus.Lineac irradiation of a total dose of 5, 000 rads combined with chemotherapies wasperformed, but the patient died 5 months later by massive, multiple metastases in bothlungs.Eleven case reports of primary malignant melanoma of the esophagus, appearing inthe literature in Japan, were reviewed.Histopathologic characteristics, clinical course and recent advances in the treatment of malignant melanoma of the esophagus were briefly discussed.
Jet mass and substructure of inclusive jets in $ \sqrt {s} = 7\;{\text{TeV}} $ pp collisions with the ATLAS experiment (2012)

A bstract Recent studies have highlighted the potential of jet substructure techniques to identify the hadronic decays of boosted heavy particles. These studies all rely upon the assumption that the internal substructure of jets generated by QCD radiation is well understood. In this article, this assumption is tested on an inclusive sample of jets recorded with the ATLAS detector in 2010, which corresponds to 35 pb −1 of pp collisions delivered by the LHC at $ \sqrt {s} = 7\;{\text{TeV}} $ . In a subsample of events with single pp collisions, measurements corrected for detector efficiency and resolution are presented with full systematic uncertainties. Jet invariant mass, k t splitting scales and N -subjettiness variables are presented for anti- k t R = 1.0 jets and Cambridge-Aachen R = 1.2 jets. Jet invariant-mass spectra for Cambridge-Aachen R = 1.2 jets after a splitting and filtering procedure are also presented. Leading-order parton-shower Monte Carlo predictions for these variables are found to be broadly in agreement with data. The dependence of mean jet mass on additional pp interactions is also explored.
Speeding up training with tree kernels for node relation labeling (2005)

We present a method for speeding up the calculation of tree kernels during training. The calculation of tree kernels is still heavy even with efficient dynamic programming (DP) procedures. Our method maps trees into a small feature space where the inner product, which can be calculated much faster, yields the same value as the tree kernel for most tree pairs. The training is sped up by using the DP procedure only for the exceptional pairs. We describe an algorithm that detects such exceptional pairs and converts trees into vectors in a feature space. We propose tree kernels on marked labeled ordered trees and show that the training of SVMs for semantic role labeling using these kernels can be sped up by a factor of several tens.
WebBase: An intranet application development system (1996)

NTT has developed WebBASE, which integrates the WWW with relational databases, and which makes data in business databases available through WWW information pages. How WebBASE allows us to develop lntranets easier, faster and less expensive is shown and is evaluated.
Vitamin D intake during the first 4 years and onset of asthma by age 5: A nested case-control study (2017)

Background
Early life vitamin D intake has been linked to asthma risk in childhood, but the role of longitudinal vitamin D exposure has not been previously evaluated. We investigated the association between vitamin D intake during the first 4 years of life and asthma risk by age 5.

Methods
Within a Finnish population-based birth cohort, 182 incident asthma cases were matched to 728 controls on sex, genetic risk for type 1 diabetes, delivery hospital, and time of birth. Vitamin D intake was assessed by age-specific 3-day food records. Parents completed a validated version of the International Study of Asthma and Allergies in Childhood questionnaire at 5 years.

Results
At 3 months, supplements were the main source of vitamin D intake; intake from foods increased from 3 months on, mainly from fortified milk products. Vitamin D intake at each specific age was associated with an increased risk of any asthma, atopic and non-atopic asthma, but only intake at 1 and 2 years was statistically significantly associated with asthma. Longitudinal vitamin D intake was associated with an increased risk of asthma (OR 1.24; 95%CI 1.00-1.53)

Conclusions
Increased vitamin D intake in childhood, particularly intake at 1 and 2 years of age, may increase risk of childhood asthma. This might reflect a true effect or residual confounding by lifestyle or environmental factors. Repeated assessment of vitamin D intake allowed evaluation of the longitudinal and age-dependent impact of vitamin D on the risk of asthma. Further longitudinal studies are required to confirm or question these findings.

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Detection of Multiple Reactive Protein Species by Immunoblotting after Recombinant Outer Surface Protein A Lyme Disease Vaccination (2000)

Laboratory confirmation of the diagnosis of Lyme disease is based on the detection of an immune response to Borrelia burgdorferi. The serodiagnosis of B. burgdorferi infection is complex and may be further confounded by the immune response to the recombinant outer surface protein A (OspA) Lyme disease vaccine. To describe how the serological response to the recombinant OspA Lyme disease vaccine affects testing for antibody to B. burgdorferi, 240 specimens from 80 study subjects were obtained at defined intervals after recombinant OspA Lyme disease vaccination. Samples were tested by indirect enzyme-linked immunosorbent assay (ELISA), antibody capture enzyme immunoassay (EIA), and Western blotting (WB). After recombinant OspA Lyme disease vaccination, ELISA for 98% of the study subjects revealed reactivity. WB with use of OspA-containing B. burgdorferi strains as sources of antigens demonstrated multiple bands. Results of testing with a US Food and Drug Administration-approved WB kit showed homogeneous reactivity in the molecular weight region >30 kDa. Testing with OspA-free strains completely eliminated all vaccine-associated reactivity by both antibody capture EIA and WB.
Mechanical Stimulation Enhances Collagen Synthesis in Periosteum-Derived Cartilage (2009)

High prevalence of osteoarthritis and poor intrinsic healing capacity of articular cartilage create a demand for cell-based strategies for cartilage repair. It is possible to tissue engineer cartilage with almost native proteoglycan content, but collagen reaches only 15% to 35% of the native content. Also its natural arcade-like structural organization is not reproduced. These drawbacks contribute to its insufficient load-bearing properties. It is generally believed that the application of mechanical loading during culturing will improve the mechanical properties. However, a suitable mechanical loading regime has not yet been established.