gebhart/patrepeval huggingface dataset:
Clustered Standard Deviation and Its Benefit to Identify Atrial Fibrillation (2019)

Background: Atrial fibrillation (AF) is a dysfunction of heart atriums shown as irregular heart activity leading to a higher risk of heart failure. Since AF may occur episodically, it is usually diagnosed using ECG Holter recordings. However, the presence of other pathologies and noise makes the automated processing of ECG Holter recordings complicated. Here, we present a new feature to distinguish AF from sinus rhythm as well as from other pathologies: Clustered Standard Deviation (C STD ).Method: QRS complexes are extracted from the ECG signal, and inter-beat intervals (RR) are ordered by their length. Then, RR clusters are found and the mean RR value is computed for each RR cluster. C STD is computed using a formula for standard deviation using cluster-specific mean values instead of a global mean.Results: C STD was evaluated for 7,254 ECG segments from a private dataset (MDT company, Brno, Czechia), 60 seconds length, 1-lead, 250 Hz sampling frequency. C STD showed high values for AF while remaining low for other pathologies and sinus rhythm. C STD between AF and other classes showed AUC 0.95. For comparison, a standard deviation of RR intervals leads to AUC 0.65 due to its sensitivity to other pathologies. Test on public MIT-AFDB dataset shown AUC and AUPRC 0.98 and 0.97, respectively.
Adaptive Blocking: Learning to Scale Up Record Linkage (2006)

Many data mining tasks require computing similarity between pairs of objects. Pairwise similarity computations are particularly important in record linkage systems, as well as in clustering and schema mapping algorithms. Because the number of object pairs grows quadratically with the size of the dataset, computing similarity between all pairs is impractical and becomes prohibitive for large datasets and complex similarity functions. Blocking methods alleviate this problem by efficiently selecting approximately similar object pairs for subsequent distance computations, leaving out the remaining pairs as dissimilar. Previously proposed blocking methods require manually constructing an index- based similarity function or selecting a set of predicates, followed by hand-tuning of parameters. In this paper, we introduce an adaptive framework for automatically learning blocking functions that are efficient and accurate. We describe two predicate-based formulations of learnable blocking functions and provide learning algorithms for training them. The effectiveness of the proposed techniques is demonstrated on real and simulated datasets, on which they prove to be more accurate than non-adaptive blocking methods.
Development and Validation of the Thaw-weakening Index (2004)

In northern climates, frost action is a major cause of pavement deterioration. It is well known that frost action in frost susceptible subgrade soils can cause considerable heaving in pavements. When spring thaw occurs, segregation ice melts generating high pore pressures in frost susceptible subgrades. The bearing capacity loss can be substantial, leading to important structural damage to pavement exposed to severe and uncontrolled loading conditions. Extensive research efforts have been devoted to the characterization of soils and material properties and their variation as a function of moisture and temperature variations. These research initiatives are typically conducted in the field using deflexion measurements or in the laboratory using cyclic triaxial testing. The results of these tests are used for the assessment of seasonal fatigue damage using analytical techniques to compute stresses and strains at critical location in pavement structures combined with empirical damage models. A new approach based on a mechanistic index, the thaw weakening index, is proposed. The index takes into consideration the amount of water accumulated by the freezing process, the rate of thawing in pavement layers and in the subgrade soil and the rate of consolidation of the pavement structure. Based on a number of observations found in the literature and on measurements made on test roads, good correlation was found between the index and the increase in pavement total deflection during spring thaw. A good correlation was also found between the index and the loss of stiffness (resilient modulus) of the subgrade soil. The paper will describe the theoretical development of the new index and will present correlations between the thaw-weakening index and observed weakening on in-service test roads during spring thaw.
An Archaeometallurgical Investigation on Metal Samples from the Chiaravalle Cross (2019)

The production and manufacturing techniques of metals involve expertise, and the study of ancient artifacts relies on interdisciplinary skills. Metalworking processes used in the production of jewelry masterpieces can, for example, give indications on the provenance of an ancient object of an unknown origin and the techniques used. In this regard, metallic samples from the Chiaravalle Cross (a beautiful processional cross with a complex structure, dating to the 13th century) have been studied, combining bulk and point measurements. Neutron-based experiments (like Prompt Gamma Activation Analysis and neutron diffraction) provide the bulk of the elemental and mineralogical composition, while particle induced X-ray emission analyses evidenced important details on its manufacturing techniques.
The Nitrogen-Removal Efficiency of a Novel High-Efficiency Salt-Tolerant Aerobic Denitrifier, Halomonas Alkaliphile HRL-9, Isolated from a Seawater Biofilter (2019)

Aerobic denitrification microbes have great potential to solve the problem of NO<sub>3</sub><sup>-</sup>-N accumulation in industrialized recirculating aquaculture systems (RASs). A novel salt-tolerant aerobic denitrifier was isolated from a marine recirculating aquaculture system (RAS) and identified as <i>Halomonas alkaliphile</i> HRL-9. Its aerobic denitrification performance in different dissolved oxygen concentrations, temperatures, and C/N ratios was studied. Investigations into nitrogen balance and nitrate reductase genes (<i>napA</i> and <i>narG</i>) were also carried out. The results showed that the optimal conditions for nitrate removal were temperature of 30 °C, a shaking speed of 150 rpm, and a C/N ratio of 10. For nitrate nitrogen (NO<sub>3</sub><sup>-</sup>-N) (initial concentration 101.8 mg·L<sup>-1</sup>), the sole nitrogen source of the growth of HRL-9, the maximum NO<sub>3</sub><sup>-</sup>-N removal efficiency reached 98.0% after 24 h and the maximum total nitrogen removal efficiency was 77.3% after 48 h. Nitrogen balance analysis showed that 21.7% of NO<sub>3</sub><sup>-</sup>-N was converted into intracellular nitrogen, 3.3% of NO<sub>3</sub><sup>-</sup>-N was converted into other nitrification products (i.e., nitrous nitrogen, ammonium nitrogen, and organic nitrogen), and 74.5% of NO<sub>3</sub><sup>-</sup>-N might be converted to gaseous products. The identification of functional genes confirmed the existence of the <i>napA</i> gene in strain HRL-9, but no <i>narG</i> gene was found. These results confirm that the aerobic denitrification strain, <i>Halomonas alkaliphile</i> HRL-9, which has excellent aerobic denitrification abilities, can also help us understand the microbiological mechanism and transformation pathway of aerobic denitrification in RASs.
Triple-Helical Transition State Analogues:  A New Class of Selective Matrix Metalloproteinase Inhibitors (2007)

Alterations in activities of one family of proteases, the matrix metalloproteinases (MMPs), have been implicated in primary and metastatic tumor growth, angiogenesis, and pathological degradation of extracellular matrix (ECM) components, such as collagen and laminin. Since hydrolysis of the collagen triple-helix is one of the committed steps in ECM turnover, we envisioned modulation of collagenolytic activity as a strategy for creating selective MMP inhibitors. In the present study, a phosphinate transition state analogue has been incorporated within a triple-helical peptide template. The template sequence was based on the alpha1(V)436-450 collagen region, which is hydrolyzed at the Gly(439)-Val(440) bond selectively by MMP-2 and MMP-9. The phosphinate acts as a tetrahedral transition state analogue, which mimics the water-bound peptide bond of a protein substrate during hydrolysis. The phosphinate replaced the amide bond between Gly-Val in the P1-P1' subsites of the triple-helical peptide. Inhibition studies revealed Ki values in the low nanomolar range for MMP-2 and MMP-9 and low to middle micromolar range for MMP-8 and MMP-13. MMP-1, MMP-3, and MT1-MMP/MMP-14 were not inhibited effectively. Melting of the triple-helix resulted in a decrease in inhibitor affinity for MMP-2. The phosphinate triple-helical transition state analogue has high affinity and selectivity for the gelatinases (MMP-2 and MMP-9) and represents a new class of protease inhibitors that maximizes potential selectivity via interactions with both prime and nonprime active site subsites as well as with secondary binding sites (exosites).
STAT5 activation promotes progression and chemotherapy-resistance in early T-cell precursor acute lymphoblastic leukemia (2023)

IL-7 supports the growth and chemoresistance of T-cell acute lymphoblastic leukemia (T-ALL), particularly the early T-cell precursor subtype (ETP-ALL), which frequently has activating mutations of IL-7 signaling. STAT5 is an attractive therapeutic target because it is almost universally activated in ETP-ALL, even in the absence of mutations of upstream activators such as the IL-7R, JAK and FLT3. To examine the role of activated STAT5 in ETP-ALL, we have used a Lmo2-transgenic (Lmo2Tg) mouse model in which we can monitor chemoresistant pre-leukemia (pre-LSCs) and leukemia stem cells (LSCs) that drive T-ALL development and relapse following chemotherapy. Using IL-7R-deficient Lmo2Tg mice, we show that IL-7 signaling was not required for the formation of pre-LSCs but essential for their expansion and clonal evolution into LSCs to generate T-ALL. Activated STAT5B was sufficient for the development of T-ALL in IL-7R; Lmo2Tg mice, indicating that inhibition of STAT5 is required to block the supportive signals provided by IL-7. To further understand the role of activated STAT5 in LSCs of ETP-ALL, we developed a new transgenic mouse that enables T-cell specific and doxycycline-inducible expression of the constitutively activated STAT5B1*6 mutant. Expression of STAT5B1*6 in T-cells had no effect alone but promoted expansion and chemoresistance of LSCs in Lmo2Tg mice. Pharmacologic inhibition of STAT5 with Pimozide induced differentiation and loss of LSCs, whilst enhancing response to chemotherapy. Furthermore, Pimozide significantly reduced leukemia burden in vivo and overcame chemoresistance of patient-derived ETP-ALL xenografts. Overall, our results demonstrate that STAT5 is an attractive therapeutic target for eradicating LSCs in ETP-ALL.
The Boulton–Katritzky rearrangement of isocarboxazid (2009)

Abstract magnified image Isocarboxazid rearranges on heating to 5‐acetonyl‐2‐benzyl‐4‐hydroxy‐1,2,3‐triazole in DMF at 150°C, in the ionic liquid, [bmin]HSO at 100°C or as a melt at 105°C. This is the first reported example of the Boulton–Katritzky rearrangement of an acyl hydrazide. J. Heterocyclic Chem., (2009)
Therapeutic Applications for Ligands of Retinoid Receptors (2000)

Synthetic retinoids, ligands for the RAR and RXR members of the steroid/thyroid superfamily of nuclear hormone receptors, are used for the treatment of psoriasis, acne, photoaging and cancer. Retinoid mechanisms of action for these conditions largely involve effects on epithelial differentiation and modulation of inflammation with some impact on the immune system. Retinoid medicinal chemistry in recent years has identified ligands highly specific for one of the three RAR subtypes (RAR-alpha) and for the RXR family of receptors, as well as antagonists for the RARs, RARalpha and the RXRs. Structure-activity relationships among the novel retinoid classes are reviewed along with potential therapeutic activities and side effects. RAR-alpha specific retinoids inhibit cancer cell growth but lack other retinoid toxicities, including skin irritation now ascribed to RAR-gama. RXR-specific retinoids lower blood glucose in animal models of type 2 diabetes albeit with a potential for mild hypothyroidism. Function-selective retinoids, especially a class of RAR antagonists called inverse agonists, have unexpected gene regulatory activity. Given the diverse properties and tissue distributions of the retinoid receptors, synthesis of additional classes of receptor-specific and function-selective ligands has the potential to produce novel therapeutic applications.
A New Prenylated Flavonol from the Roots of Sophora flavescens (1998)

A new prenylated flavonol, sophoflavescenol (1), together with five known flavonoids, kurarinol, kushenol K, kushenol H, trifolirhizin, and kuraidin, were isolated from the roots of Sophora flavescens. The structure of 1 was determined by spectroscopic analysis. Among the five known flavonoids, kurarinol, kushenol K, and kushenol H showed weak antiviral activity against Herpes simplex virus types I and II.
Advanced Processing Sequence for 3-D THz Imaging (2016)

In this paper, we present an advanced image processing sequence to perform nondestructive inspection from 3-D terahertz (THz) images. We develop all the steps starting from a 3-D tomographic reconstruction of a sample from radiographs acquired with a monochromatic millimeter-wave imaging system to an automated segmentation, extracting the different volumes of interest (VOI) composing the sample. This leads to 3-D visualization and dimensional measurements. This inspection is completed by a skeletonization and caliber analysis providing an accurate assessment of the structure, geometry, and morphology of the acquired object. Overall sequence is implemented onto an unique software and validated through different sample analysis.
High-Risk Human Papillomavirus DNA Detected in Primary Squamous Cell Carcinoma of Urinary Bladder (2013)

High-risk HPV DNA is detectable in a subset of primary bladder SCCs. Based on the well-documented carcinogenic potential of HR-HPV, there is a necessity for additional studies to investigate the role of HR-HPV in bladder carcinogenesis.
Preparation of optically pure α-methyl-α-amino acids via alkylation of the nickel(II) Schiff base of (R,S)-alanine with (S)-2-N-(N′-benzylprolyl)aminobenzaldehyde (1985)

Chiral nickel(II) complexes of Ala with (S)-2-N-(N′-benzylprolyl)aminobenzaldehyde [(S)-bba] were alkylated with alkyl halides and the diastereoisomeric complexes formed were separated on SiO2; their decomposition led to the isolation of enantiomerically pure (R)- and (S)-α-alkyl-α-amino acids with recovery of the initial (S)-bba.
Juvenile and moulting hormones from nematodes (1973)

Juvenile hormone and its analogues inhibited growth of Panagrellus redivivus and of the free-living stages of Haemonchus contortus . Substances extracted from nematodes had similar actions and also showed the activity of juvenile hormone in insects. Partly purified material from 1 g of freezedried juveniles of H. contortus contained about 200 Tenebrio units.
Vectors for RNAi Technology in Poplar (2004)

The potential of double-stranded RNA interference (RNAi) technology was studied for down-regulation of gene expression in poplar. A set of vectors was constructed generating RNAs capable of duplex formation of sequences specific for the beta-glucuronidase (GUS) reporter gene system. These gene cassettes are driven by the CaMV-35S promoter. To address the question of gene silencing, we tested the functionality of these vectors, both in transient assays by transforming protoplasts with the RNAi constructs, and in stably transformed GUSexpressing poplar plants. Agrobacterium-mediated transformation of those GUS-expressing plants with a GUS-specific RNAi construct showed a strong down-regulation of the reporter gene. From these results we conclude that RNAi is also functional in poplar.
Filamentation and restoration of normal growth in E.coli using a combined CRISPRi sgRNA/antisense RNA approach (2018)

Abstract CRISPR interference (CRISPRi) using dCas9/sgRNA is a powerful tool for the exploration and manipulation of gene functions. Here we quantify the reversible switching of crucial cellular processes by CRISPRi and an antisense RNA mechanism. Reversible induction of filamentous growth in E. coli has been recently demonstrated by controlling the expression levels of the bacterial cell division proteins FtsZ/FtsA via CRISPRi. If FtsZ falls below a critical level, cells cannot divide. However, the cells remain metabolically active and continue with DNA replication. We surmised that this makes them amenable to an inducible antisense RNA strategy to counteract FtsZ inhibition. We show that both static and inducible thresholds can adjust the characteristics of the switching process. Combining bulk data with single cell measurements, we clarify the role of bacterial heterogeneity and population dynamics for gene circuits affecting cell division. Filamentation is shown to strongly increase gene expression variability in the bacteria. Furthermore, we find reversible switching only in a small subpopulation of the bacteria, which takes over the population upon continued cell division. Successful restoration of division occurs faster in the presence of antisense sgRNAs than upon simple termination of CRISPRi induction.
Longterm Outcomes after Combat Casualty Emergency Department Thoracotomy (2009)

In the combat casualty with penetrating injury, arriving with signs of life, receiving CPR, and undergoing EDT, longterm survival with normal neurologic outcomes is possible. CPR is not a contraindication to performance of EDT in penetrating injuries if signs of life are present. A large amount of blood products are used in the resuscitation of EDT patients.
<title>Further investigation into the effects of lossy compression using free-response methodology</title> (1995)

Using free-response methodology, we measured the comparative performance of trained observers for the task of detecting simulated pulmonary nodules in computed radiographic chest images that were compressed using the full-frame discrete cosine transform algorithm. six observers read fifty-one images containing a total of 372 simulated lesions of size ranging from 8 mm to 12 mm and with six different contrasts. The images were compressed to an average of 15:1 with the same parameters that were used in an earlier two-alternative forced- choice analysis. The results showed this level of compression did not increase the number of false=positive calls per image. also, observers tended to ignore the lowest contrast nodules in all images. At low contrast we expect compression to have the greatest effect. Therefore, overall performance was not degraded by the compression process, although performance was compromised at very low contrast.
Use of Citric Acid Esters as Alternative Fuel for Diesel Engines (2013)

Common fuels for (adapted) diesel engines are fossil diesel fuel, fatty acid methyl ester (FAME or biodiesel) or vegetable oils. Further potential biogenic substitutes are the citric acid esters tributylcitrate (TBC) and triethylcitrate (TEC). Their use as fuel was applied for a patent in Germany in 2010. Proposed advantages are low soot combustion, independence of energy imports due to the possibility of local production and a broad raw material base. Comparison of their properties with relevant fuel standards showed, that only some of the demands are met. However, few rapeseed oil characteristics (e. g. oxidation stability and viscosity) can be improved if the citric acid esters are used as a blend component. The operating and emission behaviour of a vegetable oil compatible CHP unit fuelled with various rapeseed oil/TBC blends were investigated and a trouble free and soot emission reduced engine operation due to the high molecularly bound oxygen content was observed. Long term test runs are necessary for an entire technical validation.
Radiolabeled choline PET/CT before salvage lymphadenectomy dissection (2016)

To provide a systematic review of recently published reports and carry out a meta-analysis on the use of radiolabeled choline PET/computed tomography (CT) as a guide for salvage lymph node dissection (sLND) in prostate cancer patients with biochemical recurrence after primary treatments. Bibliographic database searches, from 2005 to May 2015, including Pubmed, Web of Science, and TripDatabase, were performed to find studies that included only patients who underwent sLND after radiolabeled choline PET/CT alone or in combination with other imaging modalities. For the qualitative assessment, all studies including the selected population were considered. Conversely, for the quantitative assessment, articles were included only if absolute numbers of true positive, true negative, false positive, and false negative test results were available or derivable from the text for lymph node metastases. Reviews, clinical reports, and editorial articles were excluded from analyses. Eighteen studies fulfilled the inclusion criteria and were assessed qualitatively. A total of 750 patients underwent radiolabeled choline (such as C-choline or F-choline) PET/CT before sLND. A quantitative evaluation was performed in nine studies. A patient-based, a lesion-based, and a site-based analysis was carried out in nine, four, and five studies, respectively. The pooled sensitivities were 85.3% [95% confidence interval (CI): 78.5-90.3%], 56.2% (95% CI: 41.6-69.7%), 75.3% (95% CI: 56.6-87.7%), and 63.7% (95% CI: 41-81.6%), respectively, for patient-based, lesion-based, pelvic site-based, and retroperitoneal site-based analysis. The pooled positive predictive values (PPVs) were 75% (95% CI: 68-80.9%), 85.8% (95% CI: 66.8-94.8%), 81.2% (95% CI: 70.1-88.9%), and 75.2% (95% CI: 58.7-86.7%), respectively, in the same analyses. High heterogeneities among the studies were found for sensitivities and PPVs ranging between 61.7-93.3% and 60.6-94.5%, respectively. Radiolabeled choline PET/CT has only a moderate sensitivity for the detection of metastatic lymph nodes in patients who are candidates for sLND, although the pooled PPVs ranged between 75 and 85.8% for all type of subanalyses. The presence of high heterogeneity among the studies should be considered carefully.