gebhart/patrepeval huggingface dataset:
Molecular analysis of a Clostridium butyricum NCIMB 7423 gene encoding 4-α-glucanotransferase and characterization of the recombinant enzyme produced in Escherichia coli (1997)

An Escherichia coli clone was detected in a Clostridium butyricum NCIMB 7423 plasmid library capable of degrading soluble amylose. Deletion subcloning of its recombinant plasmid indicated that the gene(s) responsible for amylose degradation was localized on a 1.8 kb NspHI-Scal fragment. This region was sequenced in its entirety and shown to encompass a large ORF capable of encoding a protein with a calculated molecular mass of 57,184 Da. Although the deduced amino acid sequence showed only weak similarity with known amylases, significant sequences identity was apparent with the 4-alpha-glucano-transferase enzymes of Streptococcus pneumoniae (46.9%), potato (42.9%) and E. coli (16.2%). The clostridial gene (designated maIQ) was followed by a second ORF which, through its homology to the equivalent enzymes of E. coli and S. pneumoniae, was deduced to encode maltodextrin phosphorylase (MaIP). The translation stop codon of MaIQ overlapped the translation start codon of the putative maIP gene, suggesting that the two genes may be both transcriptionally and translationally coupled. 4-alpha-Glucanotransferase catalyses a disproportionation reaction in which single or multiple glucose units from oligosaccharides are transferred to the 4-hydroxyl group of acceptor sugars. Characterization of the recombinant C. butyricum enzyme demonstrated that glucose, maltose and maltotriose could act as acceptor, whereas of the three only maltotriose could act as donor. The enzyme therefore shares properties with the E. coli MaIQ protein, but differs significantly from the glucanotransferase of Thermotoga maritima, which is unable to use maltotriose as donor or glucose as acceptor. Physiologically, the concerted action of 4-alpha-glucanotransferase and maltodextrin phosphorylase provides C. butyricum with a mechanism of utilizing amylose/maltodextrins with little drain on cellular ATP reserves.
Methylation-Independent Silencing of the Tumor Suppressor <i>INK4b</i> (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16) (2007)

The tumor suppressor gene INK4b (p15) is silenced by CpG island hypermethylation in most acute myelogenous leukemias (AML), and this epigenetic phenomenon can be reversed by treatment with hypomethylating agents. Thus far, it was not investigated whether INK4b is hypermethylated in all cytogenetic subtypes of AML. A comparison of levels of INK4b methylation in AML with the three most common cytogenetic alterations, inv(16), t(8;21), and t(15;17), revealed a strikingly low level of methylation in all leukemias with inv(16) compared with the other types. Surprisingly, the expression level of INK4b in inv(16)+ AML samples was low and comparable with that of the other subtypes. An investigation into an alternative mechanism of INK4b silencing determined that the loss of INK4b expression was caused by inv(16)-encoded core binding factor beta-smooth muscle myosin heavy chain (CBFbeta-SMMHC). The silencing was manifested in an inability to activate the normal expression of INK4b RNA as shown in vitamin D3-treated U937 cells expressing CBFbeta-SMMHC. CBFbeta-SMMHC was shown to displace RUNX1 from a newly determined CBF site in the promoter of INK4b. Importantly, this study (a) establishes that the gene encoding the tumor suppressor p15(INK4b) is a target of CBFbeta-SMMHC, a finding relevant to the leukemogenesis process, and (b) indicates that, in patients with inv(16)-containing AML, reexpression from the INK4b locus in the leukemia would not be predicted to occur using hypomethylating drugs.
A polymorphism in the CYP17 gene is associated with male breast cancer (1999)

The CYP17 gene codes for the cytochrome P450c17alpha enzyme that is involved in the synthesis of oestrogens. This case-control study from the South East of Scotland shows that a polymorphism of the CYP17 gene is associated with an increased risk of male breast cancer.
Requirement of PDZ-Containing Proteins for Cell Cycle Regulation and Differentiation in the Mouse Lens Epithelium (2003)

The roles of PDZ domain-containing proteins such as Dlg and Scrib have been well described for Drosophila; however, their requirement for mammalian development is poorly understood. Here we show that Dlg, Scrib, MAGI1, MAGI3, and MPDZ are expressed in the mouse ocular lens. We demonstrate that the increase in proliferation and defects in cellular adhesion and differentiation observed in epithelia of lenses that express E6, a viral oncoprotein that can bind to several PDZ proteins, including the human homologs of Dlg and Scrib, is dependent on E6's ability to bind these proteins via their PDZ domains. Analyses of lenses from mice carrying an insertional mutation in Dlg (dlg(gt)) show increased proliferation and proliferation in spatially inappropriate regions of the lens, a phenotype similar to that of lenses expressing E6. The results from this study indicate that multiple PDZ domain-containing proteins, including Dlg and Scrib, may be required for maintaining the normal pattern of growth and differentiation in the lens. Furthermore, the phenotypic similarities among the Drosophila dlg mutant, the lenses of dlg(gt) mice, and the lenses of E6 transgenic mice suggest that Dlg may have a conserved function in regulating epithelial cell growth and differentiation across species.
Carbapenem resistance among Gram-negative isolates collected from patients in ICU and non-ICU hospital wards in Hong Kong: SMART 2017–2020 (2023)

Carbapenem-nonsusceptible isolates of P. aeruginosa were common (>15% of isolates). P. aeruginosa percent susceptible values for ceftolozane/tazobactam (97.3% susceptible overall) were ≥14% higher than those for carbapenems in both ICU and non-ICU isolates. Carbapenemases were rare among both P. aeruginosa (one isolate) and Enterobacterales (three isolates). Most Enterobacterales isolates tested from ICU and non-ICU patients in Hong Kong hospitals in 2017-2020 were susceptible to meropenem and ertapenem (≥98%); imipenem was less active (89% susceptible).
Laser cladding using high-power diode lasers (1998)

Currently, intricate problems of surface treatment can be solved through precision cladding using advanced laser technology. However, the high price of CO2 and Nd:YAG lasers, the effort required for beam guiding as well as the low absorption of the CO2 irradiation limit the applications. In light of this, a new and promising solution is provided by the current availability of high-power diode lasers: it makes laser cladding essentially more efficient and practicable. By one-step cladding with a 1.4 kW diode laser, protection layers of Co-based alloys, a carbide-reinforced Ni alloy, and alumina can be deposited onto steels and aluminium-based light alloys. The width of single tracks is up to 5 mm, with a layer thickness of 0.2 to 1.5 mm. For tasks of repair and remanufacturing, multilayer stacking of metal alloys can be easily performed. The layers are dense and with a fine dendritic structure and are metallurgically or chemically bonded to the substrate. For the Co- and Ni-based alloys, the cladding rate is 0.5 kg/h. This high value is due to the higher absorption degree of the 0.94 μm diode irradiation compared to the 10.6 μm CO2 irradiation. Comparison of the cladding results for tracks produced with CO2 and diode lasers has shown that 1.4 kW diode power is equivalent to 3.9 kW CO2 laser power. Thus, the absorption obviously increases by a factor of at least 2.5. In addition to the higher efficiency, the resulting tracks appear to be of better quality. Thus far, examples of applications are the repair of wear-damaged punches and dies, and the hardfacing of engine valves.
Model-driven Approach for Privacy Management in Business Ecosystem (2017)

Protection of individuals with regard to the processing of personal data and the free movement of such data constitutes new challenges in terms of privacy management. Although this privacy management ought to be conducted in compliance with national and international regulation, for now we observe that no solution, model or method, fully consider and integrate these new regulations yet. Therefore, in this paper, we propose to tackle this problem through the definition of an expressive privacy metamodel which aims to represent and aggregate the concepts that are relevant to define and to deal with privacy issues, at an organizational level. Secondly, we discuss how this privacy metamodel may support and may help understanding the management of the privacy in enterprises involve in interconnected societies, by integrating the privacy metamodel with the systemic business ecosystem.
Operative risk of mitral valve replacement: discriminant analysis of 1329 procedures. (1985)

The influence of 34 variables on the operative mortality rate for isolated mitral valve replacement (MVR) was assessed by univariate and multivariate logistic regression analysis. The physiologic lesions were classified as stenosis (20%, operative mortality rate 8 +/- 1%), regurgitation (44%, operative mortality rate 13 +/- 2%), and mixed (34%, operative mortality rate 8 +/- 1%). Functional class (NYHA), previous myocardial infarction, and hepatic dysfunction were powerful independent clinical determinants of operative mortality (p less than .001), along with age at operation and emergency operation (p = .001, p = .04). Concomitant coronary artery bypass grafting or tricuspid annuloplasty, angina, ischemic etiology, and physiologic lesion were not significant independent determinants of operative risk. Interestingly, year of operation, prosthetic valve dysfunction, and previous cardiac surgery had no important effect on operative mortality. Early operative risk for MVR was related to preoperative cardiac and hepatic function. Prior myocardial infarction substantially increased the risk even if the mitral valve disease was not ischemic in origin. Increased operative mortality rate in the subgroup with mitral regurgitation was related to advanced left ventricular failure and myocardial infarction rather than the etiology of the mitral regurgitation. These clinical factors coupled with more refined measurements of left ventricular systolic pump function (independent of loading conditions) should permit more intelligent decision making regarding the optimal timing of MVR, at least in terms of early operative risk.
Self‐Repair of a One‐Dimensional Molecular Assembly in Mesoporous Silica by a Nanoscopic Template Effect (2010)

Upon confinement of a trinuclear gold(I) pyrazolate complex in a hexagonal silicate channel, the luminescence center formed by a AuI–AuI metallophilic interaction is not only protected against thermal disruption but also strongly encouraged to self-recover from a heat-induced structural damage. This nanoscopic template effect is negligible for a lamellar silica framework.
AGC and DCOC algorithms for sliding IF non-coherent ULP wireless receiver (2016)

We consider joint radio frequency and baseband physical (PHY) layer algorithms for ultra low power (ULP) wireless communications. Our focus is on the design of automatic gain control (AGC) and direct current offset compensation (DCOC) algorithms for non-coherent reception based on processing analog to digital converter output samples only. Specifically, we jointly design and evaluate AGC and DCOC algorithms for sliding intermediate frequency non-coherent wireless receiver with IEEE 802.15.4q ULP PHY packet format.
Influence of the sequence of atrioventricular and interventricular delay optimization on acute response to CRT (2013)

In CRT, the optimal AV and VV delays and the acute hemodynamic response are similar
in a majority of patients when comparing matrix and sequential optimization strategies.
Since matrix optimization is very time consuming, we do not advise to use this strategy
in standard practice.
S-Beacon: Next generation BLE beacon solution for enhanced personalization (2016)

We introduce next generation Bluetooth Low Energy (BLE) [1] Beacon solution called S-Beacon that opens a new business opportunity by globally interconnecting smartphone users with next generation personalization services. S-Beacon is a BLE based technology on smartphones and wearables to indicate user presence along with personal preferences and demographic data that serves as a key factor for enhanced personalized services. This paper discusses its enhanced BLE based proximity, optimized resource consumption, and manageability of beacon devices. We envision that the S-Beacon solution is well suited for a wide range of business sectors such as retail store, public place, hotel, hospital and home.
Gene-chromatin regulatory circuits driving stemness in the anterior pituitary (2022)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Reaction of Photoisomerized Azonaphthalenes with Acetyl Chloride (1977)

Irradiation of the solutionof azonaphthalenes in acetyl chloride results in the formation of monochlorinated N, N'-diacetylhydrazonaphthalenes which are the mixtures of two positional isomers with respect to the chlorine substitution. A similar reaction of naphthaleneazobenzenes gives the chlorinated products in which the attack of the naphthalene ring predominates. These facts can be interpreted in terms of the resonance stabilization of nitrenium ions. The α- and β-substituted naphthalene rings show equal reactivity towards the chlorination.
Increased plasma concentrations of adrenomedullin correlate with relaxation of vascular tone in patients with septic shock (1997)

Enhanced production of adrenomedullin in patients with septic shock may contribute to reduced vascular tone, hypotension, or both. More data are needed to clarify the role of adrenomedullin in the regulation of vascular tone in this patient population.
Unobtrusive real-time heart rate variability analysis for the detection of orthostatic dysregulation (2016)

The possibilities for wearable health care technology to improve the quality of life for chronic disease patients has been increasing within recent years. For instance, unobtrusive cardiac monitoring can be applied to people suffering from a disorder of the autonomic nervous system (ANS) which show a significantly lower heart rate variability (HRV) than healthy people. Although recent work presented solutions to analyze this relationship, they did not perform it during daily life situations. For that reason, this work presents a system for a real-time analysis of the user's HRV on an Android-based mobile device throughout the day. The system was used for the detection of an orthostatic dysregulation which can be an indicator for a disorder of the ANS. Measures for HRV analysis were computed from acquired ECG data and compared before and after a posture change. For triggering the HRV analysis, an IMU-based algorithm which detects stand up events was developed. As a proof of concept for an automatic assessment of an orthostatic dysregulation, a classification based on the derived HRV measures was performed. The performance of the stand up detection was evaluated in the first part of this study. The second part was conducted for the evaluation of the derived HRV measures and involved healthy subjects as well as patients with idiopathic Parkinson's Disease. The results of the evaluation showed a recognition rate of 90.0 % for the stand up detection algorithm. Furthermore, a clear difference in the change of HRV measures between the two groups before and after standing up was observed. The classification provided an accuracy of 96.0%, and a sensitivity of 93.3%. The results demonstrated the possibility of unobtrusive HRV monitoring during daily life situations.
Shape evolution and bubble formation of acoustically levitated drops (2018)

Experiments shows that with increasing sound intensity, an acoustically levitated drop buckles into a bowl shape and experiences a drastic expansion and closure, leading to the formation of an air bubble. This is attributed to the enhanced suction effect at the film rim due to the occurrence of resonance with sound field.
Simulator-Based Self-Supervision for Learned 3D Tomography Reconstruction (2022)

We propose a deep learning method for 3D volumetric reconstruction in low-dose helical cone-beam computed tomography. Prior machine learning approaches require reference reconstructions computed by another algorithm for training. In contrast, we train our model in a fully self-supervised manner using only noisy 2D X-ray data. This is enabled by incorporating a fast differentiable CT simulator in the training loop. As we do not rely on reference reconstructions, the fidelity of our results is not limited by their potential shortcomings. We evaluate our method on real helical cone-beam projections and simulated phantoms. Our results show significantly higher visual fidelity and better PSNR over techniques that rely on existing reconstructions. When applied to full-dose data, our method produces high-quality results orders of magnitude faster than iterative techniques.
Measuring Diagnostic Accuracy for Infection in Patients Treated for Sepsis: An Important but Challenging Exercise (2023)

Sepsis remains a leading cause of death and disability.Observational studies suggest that timely antibiotic therapy is the most important treatment-related determinant of outcomes in sepsis [1][2][3][4].The Surviving Sepsis Campaign (SSC) guidelines therefore emphasize immediately administering empiric broad-spectrum antibiotics when sepsis is suspected.This recommendation is amplified by the Centers for Medicare & Medicaid's (CMS's) Severe Sepsis/Septic Shock Early Management Bundle (SEP-1) that requires clinicians to administer antibiotics within 3 hours of sepsis onset [5].Concerns have been raised, however, that these clinical and regulatory pressures create a culture of "treat first, ask questions later" for anyone with possible sepsis.Many signs and symptoms of sepsis are nonspecific to infection.Consequently, increasing pressure to treat immediately may increase overtreatment and antibiotic-related harms
From single cells to single molecules: general discussion (2016)

Mario A. Alpuche-Aviles opened a general discussion of the papers by Serge Lemay: The concentrations have to be very low and one worries about background issues and the effect of contaminants. Why do they have to be this low? Could these experiments be performed at higher concentrations?
PhishMatch: A Layered Approach for Effective Detection of Phishing URLs (2021)

Phishing attacks continue to be a significant threat on the Internet. Prior studies show that it is possible to determine whether a website is phishing or not just by analyzing its URL more carefully. A major advantage of the URL based approach is that it can identify a phishing website even before the web page is rendered in the browser, thus avoiding other potential problems such as cryptojacking and drive-by downloads. However, traditional URL based approaches have their limitations. Blacklist based approaches are prone to zero-hour phishing attacks, advanced machine learning based approaches consume high resources, and other approaches send the URL to a remote server which compromises user's privacy. In this paper, we present a layered anti-phishing defense, PhishMatch, which is robust, accurate, inexpensive, and client-side. We design a space-time efficient Aho-Corasick algorithm for exact string matching and n-gram based indexing technique for approximate string matching to detect various cybersquatting techniques in the phishing URL. To reduce false positives, we use a global whitelist and personalized user whitelists. We also determine the context in which the URL is visited and use that information to classify the input URL more accurately. The last component of PhishMatch involves a machine learning model and controlled search engine queries to classify the URL. A prototype plugin of PhishMatch, developed for the Chrome browser, was found to be fast and lightweight. Our evaluation shows that PhishMatch is both efficient and effective.
Construction of heparan sulfate microarray for investigating the binding of specific saccharide sequences to proteins (2020)

Heparan sulfate (HS) is a heterogeneous, extracellular glycan that interacts with proteins and other molecules affecting many biological processes. The specific binding motifs of HS interactions are of interest, but have not been extensively characterized. Glycan microarrays are valuable tools that can be used to probe the interactions between glycans and their ligands while relying on relatively small amounts of samples. Recently, chemoenzymatic synthesis of HS has been employed to produce specific HS structures that can otherwise be difficult to produce. In this study, a microarray of diverse chemoenzymatically synthesized HS structures was developed and HS interactions were characterized. Fluorescently labeled antithrombin III (AT) and fibroblast growth factor-2 (FGF2) were screened against 95 different HS structures under three different printing concentrations to confirm the utility of this microarray. Specific sulfation patterns were found to be important for binding to these proteins and results are consistent with previous specificity studies. Furthermore, the binding affinities (KD,surf) of AT and FGF2 to multiple HS structures were determined using a microarray technique and is consistent with previous reports. Lastly, the 95-compound HS microarray was used to determine the distinct binding profiles for interleukin 12 and platelet factor 4. This technique is ideal for rapid expansion and will be pivotal to the high-throughput characterization of biologically important structure/function relationships.
Towards next generation Intervention Autonomous Underwater Vehicles (I-AUV): development of innovative mobile manipulation techniques (2015)

Autonomous underwater manipulation with free floating base is still an open topic of research; dynamic manipulation tasks, executed maintaining relevant vehicle velocities, offer an additional challenge. The focus of this paper is the modelling and the control of an Intervention Autonomous Underwater Vehicle (I-AUV). An accurate model of the whole system has been developed, including vehicle-fluid interaction. A control strategy for the whole I-AUV system is proposed, comprising a suitable grasp planning strategy. The performances of the I-AUV control system have been analysed in details by means of simulation of a dynamic manipulation task.
A set of tournaments with many Hamiltonian cycles (2012)

For a random tournament on $3^n$ vertices, the expected number of Hamiltonian cycles is known to be $(3^n -1)!/2^{3^n}$. Let $T_1$ denote a tournament of three vertices $ {v_1, v_2, v_3}$. Let the orientation be such that there are directed edges from $v_1 $to $v_2$ , from $v_2$ to $v_3$ and from $v_3$ to $ v_1$. Construct a tournament $T_i$ by making three copies of $T_{i-1}$, $T_{i-1}'$, $T_{i-1}''$ and $T_{i-1}'''$. Let each vertex in $T_{i-1}'$ have directed edges to all vertices in $T_{i-1}''$, similarly place directed edges from each vertex in $T_{i-1}''$ to all vertices in $T_{i-1}'''$ and from $T_{i-1}'''$ to $T_{i-1}'$. In this thesis, we shall study this family of highly symmetric tournaments. In particular we shall present two different algorithms to calculate the number of Hamiltonian cycles in these tournaments and compare them with the expected number and with known bounds for random tournaments. This thesis is motivated by the question of the maximum number of Hamiltonian cycles a tournament can have.