gebhart/patrepeval huggingface dataset:
Domain organization, folding and stability of bacteriophage T4 fibritin, a segmented coiled‐coil protein (2002)

Fibritin is a segmented coiled-coil homotrimer of the 486-residue product of phage T4 gene wac. This protein attaches to a phage particle by the N-terminal region and forms fibrous whiskers of 530 A, which perform a chaperone function during virus assembly. The short C-terminal region has a beta-annulus-like structure. We engineered a set of fibritin deletion mutants sequentially truncated from the N-termini, and the mutants were studied by differential scanning calorimetry (DSC) and CD measurements. The analysis of DSC curves indicates that full-length fibritin exhibits three thermal-heat-absorption peaks centred at 321 K (Delta H=1390 kJ x mol trimer(-1)), at 336 K (Delta H=7600 kJ x mol trimer(-1)), and at 345 K (Delta H=515 kJ x mol trimer(-1)). These transitions were assigned to the N-terminal, segmented coiled-coil, and C-terminal functional domains, respectively. The coiled-coil region, containing 13 segments, melts co-operatively as a single domain with a mean enthalpy Delta Hres=21 kJ x mol residue(-1). The ratio of Delta HVH/Delta Hcal for the coiled-coil part of the 120-, 182-, 258- and 281-residue per monomer mutants, truncated from the N-termini, and for full-length fibritin are 0.91, 0.88, 0.42, 0.39, and 0.13, respectively. This gives an indication of the decrease of the 'all-or-none' character of the transition with increasing protein size. The deletion of the 12-residue-long loop in the 120-residue fibritin increases the thermal stability of the coiled-coil region. According to CD data, full-length fibritin and all the mutants truncated from the N-termini refold properly after heat denaturation. In contrast, fibritin XN, which is deleted for the C-terminal domain, forms aggregates inside the cell. The XN protein can be partially refolded by dilution from urea and does not refold after heat denaturation. These results confirm that the C-terminal domain is essential for correct fibritin assembly both in vivo and in vitro and acts as a foldon.
High Resolution Time Difference of Arrival Using Timestamps for Localization in 802.11b/g Wireless Networks (2010)

Localization of mobile devices is an area of much interest in both the commercial, and government sectors. One particular method of localization uses time-difference of arrival (TDoA) measurements from multiple receivers. This can be done using shared timestamps indicating the time of arrival (ToA) among distributed receivers. High resolution timestamps are particularly important to ensure reasonable spatial resolution of the localization method. This paper presents a method to obtain high-resolution time-of-arrival stamps for 802.11b frames based on matched filtering and time-averaged power. This method can be extended to the higher data rates used by 802.11g.
Multiplexed and Robust Representations of Sound Features in Auditory Cortex (2011)

We can recognize the melody of a familiar song when it is played on different musical instruments. Similarly, an animal must be able to recognize a warning call whether the caller has a high-pitched female or a lower-pitched male voice, and whether they are sitting in a tree to the left or right. This type of perceptual invariance to "nuisance" parameters comes easily to listeners, but it is unknown whether or how such robust representations of sounds are formed at the level of sensory cortex. In this study, we investigate whether neurons in both core and belt areas of ferret auditory cortex can robustly represent the pitch, formant frequencies, or azimuthal location of artificial vowel sounds while the other two attributes vary. We found that the spike rates of the majority of cortical neurons that are driven by artificial vowels carry robust representations of these features, but the most informative temporal response windows differ from neuron to neuron and across five auditory cortical fields. Furthermore, individual neurons can represent multiple features of sounds unambiguously by independently modulating their spike rates within distinct time windows. Such multiplexing may be critical to identifying sounds that vary along more than one perceptual dimension. Finally, we observed that formant information is encoded in cortex earlier than pitch information, and we show that this time course matches ferrets' behavioral reaction time differences on a change detection task.
Advanced capabilities of the outer join (1992)

This paper demonstrates that the modeling of complex data structures can be performed easily and naturally in SQL using the direct outer join operation as defined in the proposed ISO-ANSI SQL2 standard. This paper goes on to demonstrate four advanced capabilities that can be implemented by SQL vendors utilizing the data modeling ability of the outer join. These capabilities are: powerful optimization techniques that can dynamically shorten the access path length; intelligent join view updates that utilize the semantics in the data structure being modeled; direct disparate heterogeneous database access that is transparent and efficient; and automatic conversion of multi-table structures into nested relations allowing for more powerful SQL operations.
Repeatable runout disturbance compensation with a new data collection method for hard disk drive (2005)

In this paper, a new method to determine repeatable runout (RRO) disturbance data is proposed. The obtained RRO disturbance data is further used to compensate for the RRO disturbance. The error transfer function (or sensitivity function) can be obtained without any additional instrument, and moreover the estimated RRO disturbance obtained from the proposed method will not be affected by the variation of the actuator model. Furthermore, the proposed method is much easier to be implemented than the fast Fourier transform and inverse fast Fourier transform (FFT/IFFT) method as much less computation is needed. Experimental results show that the servo tracking performance can be significantly improved by using the estimated disturbance to compensate the actual RRO disturbances. Comparative study between the proposed RRO compensation method and the iterative learning control (ILC)-based compensation method has also been performed in this paper.
Active microscopic cellular image annotation by superposable graph transduction with imbalanced labels (2008)

Systematic content screening of cell phenotypes in microscopic images has been shown promising in gene function understanding and drug design. However, manual annotation of cells and images in genome-wide studies is cost prohibitive. In this paper, we propose a highly efficient active annotation framework, in which a small amount of expert input is leveraged to rapidly and effectively infer the labels over the remaining unlabeled data. We formulate this as a graph based transductive learning problem and develop a novel method for label propagation. Specifically, a label regularizer method is proposed to handle the important label imbalance issue, typically seen in the cellular image screening applications. We also design a new scheme which breaks the graph into linear superposition of contributions from individual labeled samples. We take advantage of such a superposable representation to achieve fast annotation in an interactive setting. Extensive evaluations over toy data and realistic cellular images confirm the superiority of the proposed method over existing alternatives.
Surface Acoustic Wave Driven Light Shutters Using Polymer‐Dispersed Liquid Crystals (2011)

A surface acoustic wave (SAW)-driven light shutter is demonstrated using poly­mer-dispersed liquid crystals (PDLCs). Our experiments show that a PDLC film switches from a non-transparent state to a transparent state when subjected to a SAW. The working mechanism is analyzed theoretically and the acousto-optic properties of the PDLC film are characterized. This swit­ching behavior results from the acoustic streaming-induced realignment of liquid crystal (LC) molecules as well as SAW-induced thermal diffusion. Such a device shows an excellent performance in terms of imaging quality and optical contrast, which is important for display applications and smart windows.
What the GDPR means for businesses (2016)

The long-awaited General Data Protection Regulation (GDPR) of the EU was provisionally agreed in December 2015.1 The final details are still being ironed out, but publication of the final version of the regulation is expected around July 2016.2 There will then be a two-year waiting period until every organisation that does business in, or with, the EU must comply with the regulation. Since it is a regulation, not a directive, compliance is mandatory, without the need for each member state to ratify it into its own legislation. The GDPR expands the scope of data protection so that it applies to anyone or any organisation that collects and processes information related to EU citizens, no matter where they are based or where the data is stored. Colin Tankard of Digital Pathways examines what effect the new regulation is likely to have on organisations.
Novel Daptomycin Combinations against Daptomycin-Nonsusceptible Methicillin-Resistant <i>Staphylococcus aureus</i> in an <i>In Vitro</i> Model of Simulated Endocardial Vegetations (2010)

Reduced susceptibility to daptomycin has been reported in patients with infections due to methicillin-resistant Staphylococcus aureus (MRSA). Although infections with daptomycin-nonsusceptible (DNS) MRSA are infrequent, optimal therapy of these strains has not been determined. We investigated the killing effects of novel antibiotic combinations with daptomycin (DAP) against two clinical DNS MRSA isolates (SA-684 and R6003) in a 72-h in vitro pharmacokinetic/pharmacodynamic (PK/PD) model with simulated endocardial vegetations (SEV). Simulated regimens included DAP at 6 mg/kg every 24 h (q24h) alone or in combination with trimethoprim-sulfamethoxazole (TMP/SMX) at 160/800 mg q12h, linezolid (LIN) at 600 mg q12h, cefepime (CEF) at 2 g q12h, and nafcillin (NAF) at 4 g q4h. Bactericidal activity was defined as a ≥3-log(10) CFU/g kill. Differences in CFU/g were evaluated between 4 and 72 h by analysis of variance with the Bonferroni post hoc test. DAP MICs were 4 and 2 mg/liter for SA-684 and R6003, respectively. In the PK/PD model, DAP alone was slowly bactericidal, achieving a 3-log(10) kill at 24 and 50 h for SA-684 and R6003, respectively. Against SA-684, DAP plus TMP/SMX, CEF, LIN, or NAF was bactericidal at 4, 4, 8, and 8 h, respectively, and maintained this activity for the 72-h study duration. DAP plus TMP/SMX or CEF exhibited superior killing than DAP alone against SA-684 between 4 and 72 h, and overall this was significant (P < 0.05). Against R6003, DAP plus TMP/SMX was bactericidal (8 h) and superior to DAP alone between 8 and 72 h (P < 0.001). The unique combination of DAP plus TMP/SMX was the most effective and rapidly bactericidal regimen against the two isolates tested and may provide a clinical option to treat DNS S. aureus infections.
[Mesoporous silica nanoparticles for cancer theranostic drug delivery]. (2013)

Mesoporous silica nanoparticles as drug carrier have become the new hot point in the field of biomedical application in recent years. This review focuses on the more recent developments and achievements on experimental design aspect of mesoporous silica nanoparticles with cancer diagnosis and therapy. The key advances of functionalization strategies of mesoporous silica nanoparticles with controlled release, tumor targeting and overcoming multidrug resistance are discussed in particular. Mesoporous silica nanoparticles as unique delivery systems have the potential to provide significantly a sound platform for cancer theranostic application.
Mantle cell lymphoma in leukemic phase (1999)

Recognition of the characteristic cytologic features of leukemic mantle cells can help to distinguish them from other chronic lymphoproliferative disorders. In contrast to the latter, the clinical course is aggressive and response to conventional chemotherapy is poor.
Ferulic Acid-Based Polymers with Glycol Functionality as a Versatile Platform for Topical Applications (2015)

Ferulic acid-based polymers with aliphatic linkages have been previously synthesized via solution polymerization methods, yet they feature relatively slow ferulic acid release rates (∼11 months to 100% completion). To achieve a more rapid release rate as required in skin care formulations, ferulic acid-based polymers with ethylene glycol linkers were prepared to increase hydrophilicity and, in turn, increase ferulic acid release rates. The polymers were characterized using nuclear magnetic resonance and Fourier transform infrared spectroscopies to confirm chemical composition. The molecular weights, thermal properties (e.g., glass transition temperature), and contact angles were also obtained and the polymers compared. Polymer glass transition temperature was observed to decrease with increasing linker molecule length, whereas increasing oxygen content decreased polymer contact angle. The polymers' chemical structures and physical properties were shown to influence ferulic acid release rates and antioxidant activity. In all polymers, ferulic acid release was achieved with no bioactive decomposition. These polymers demonstrate the ability to strategically release ferulic acid at rates and concentrations relevant for topical applications such as skin care products.
Handling Class Overlap and Imbalance to Detect Prompt Situations in Smart Homes (2013)

The class imbalance problem is a well-known classification challenge in machine learning that has vexed researchers for over a decade. Under-representation of one or more of the target classes (minority class(es)) as compared to others (majority class(es)) can restrict the application of conventional classifiers directly on the data. In addition, emerging challenges such as overlapping classes, make class imbalance even harder to solve. Class overlap is caused due to ambiguous regions in the data where the prior probability of two or more classes are approximately equal. We are motivated to address the challenge of class overlap in the presence of imbalanced classes by a problem in pervasive computing. Specifically, we are designing smart environments that perform health monitoring and assistance. Our solution, ClusBUS, is a clustering-based under sampling technique that identifies data regions where minority class samples are embedded deep inside majority class. By removing majority class samples from these regions, ClusBUS preprocesses the data in order to give more importance to the minority class during classification. Experiments show that ClusBUS achieves improved performance over an existing method for handling class imbalance.
No Visitor Comes Empty-Handed – Some Thoughts on Unhealthy Dependency (2013)

This article looks at a number of issues relating to Unhealthy Dependency between churches in Africa and those in the Materially Developed World. Having defined unhealthy Dependency and recognizing the significance of finance in this area, it looks at the bigger picture, identifying a number of other areas where Unhealthy Dependency has arisen and continues to be significant. It also begins to point out some of the methods by which such unhealthy dependency is being tackled.
New Global Survey Shows an Increasing Cancer Burden (2014)

Data show a 20% increase in breast cancer from 2008 to 2012.
Rotational manipulation of a yeast cell using opticalfibres (1997)

Optical trapping and rotational manipulation of a biological cell using optical fibres (singlemode fibre) is successfully demonstrated. The experimental results show that the control of the rotational manipulation of a yeast cell using two optical fibres is easily realised by controlling the output power from each trapping fibre.
Small‐fiber sensory neuropathies: Clinical course and neuropathology of idiopathic cases (1998)

We describe the clinical features, natural history, and neuropathology of 32 patients presenting with "burning feet," for whom no specific cause was identified. All had neuropathic pain in the feet and morphological abnormalities of cutaneous innervation in skin obtained using punch biopsy. Most (29) had an abnormal sensory examination. All had normal strength, proprioception, tendon reflexes, and nerve conductions. Two clinical patterns were apparent, based on natural history and spatial distribution of cutaneous denervation. Most (28) patients presented with neuropathic pain initially restricted to the feet and toes but extending more proximally to involve the legs and hands with time. Intraepidermal nerve fiber (IENF) density was most severely reduced distally, with more normal IENF densities in skin from proximal sites. In contrast, a minority (4) presented with the abrupt onset of generalized cutaneous burning pain and hyperesthesia. In these patients, IENF densities were reduced in skin from both proximal and distal sites. Absolute IENF densities in calf skin were reduced below the lower limit of normal (5th percentile) in 26 (81%). Of the 6 who underwent sural nerve biopsy, 4 had selective loss of small myelinated and/or unmyelinated axons and 2 had normal histology and fiber densities despite reduced IENF densities in skin biopsy specimens. Punch skin biopsy from proximal and distal sites is a useful means of assessing these distinctive patients and may provide further insight into pathophysiology.
Age and Sex Differences and Temporal Trends in the Use of Invasive and Noninvasive Procedures in Patients Hospitalized With Acute Myocardial Infarction (2022)

Background Few studies have examined age and sex differences in the receipt of cardiac diagnostic and interventional procedures in patients hospitalized with acute myocardial infarction and trends in these possible differences during recent years. Methods and Results Data from patients hospitalized with a first acute myocardial infarction at the major medical centers in the Worcester, Massachusetts, metropolitan area were utilized for this study. Logistic regression analysis was used to examine age (<55, 55-64, 65-74, and ≥75 years) and sex differences in the receipt of echocardiography, exercise stress testing, coronary angiography, percutaneous coronary interventions, and coronary artery bypass graft surgery, and trends in the use of those procedures during patients' acute hospitalization, between 2005 and 2018, while adjusting for important confounding factors. The study population consisted of 1681 men and 1154 women with an initial acute myocardial infarction who were hospitalized on an approximate biennial basis between 2005 and 2018. A smaller proportion of women underwent cardiac catheterization, percutaneous coronary intervention, and coronary artery bypass graft surgery, while there were no sex differences in the receipt of echocardiography and exercise stress testing. Patients aged ≥75 years were less likely to undergo cardiac catheterization, percutaneous coronary intervention, and coronary artery bypass graft surgery, but were more likely to receive echocardiography compared with younger patients. Between 2005 and 2018, the use of echocardiography and coronary artery bypass graft surgery nonsignificantly increased among all age groups and both sexes, while the use of cardiac catheterization and percutaneous coronary intervention increased nonsignificantly faster in women and older patients. Conclusions We observed a continued lower receipt of invasive cardiac procedures in women and patients aged ≥75 years with acute myocardial infarction, but age and sex gaps associated with these procedures have narrowed during recent years.
Direct assessment of the mechanical modulus of graphene co-doped with low concentrations of boron–nitrogen by a non-contact approach (2014)

Boron and nitrogen co-doping has been shown to be an effective way to induce a band gap in graphene for electrical applications but only a few theoretical studies have been done to understand the elastic and mechanical properties of the modified graphene. Until now, no experimental assessment of the mechanical modulus of boron-nitrogen-doped graphene (BNG) has been reported in the literature. Here, we demonstrate a novel non-contact approach to determine the in-plane stiffness of BNG at low BN concentrations. The in-plane stiffness of BNG with 2 at% BN concentration was estimated to be about 309 N m(-1), which is lower than that of pristine graphene, in good agreement with some theoretical studies. Moreover, we correlated the conductivity of BNG with induced strain and found the BNG to be more sensitive than pristine graphene in response to externally applied strain. This result indicates that BNG is a more suitable material than graphene for strain sensor applications.
3-D Simulation of Remote Field Eddy Current Detection for Stress Corrosion Cracks in Pipeline (2013)

Three-dimensional (3-D)finite element simulation models are conducted to simulate the in-serviceinspection of the axial stress corrosion cracking (SCC) in ferromagneticpipeline using remote field eddy current (RFEC) probes. In this paper, atypical remote field eddy current probe which is internal to and coaxial withthe pipe is firstly introduced. Then a 3-D finite element simulation model isestablished in ANSYS to analyze the detection of RFEC technology. Finally theRFEC signals are observed when changing the geometric parameters, and thedefinite influences of crack size on the amplitude and phase lag of REFCsignals are evaluated. The results of the investigations are beneficial to thedetection and sizing of SCC in pipelines
[Methodology of enacting standards for remediation of contaminated soils]. (2004)

Remediation technology for contaminated soils is being developed rapidly in recent years. However, there is a hysteresis in enacting remediation standards for contaminated soils. In particular, no corresponding research has been done in China. Methodology of enacting standards for the remediation of contaminated soils is discussed in order to promote the work in this field. It is emphasized that technological cleanup levels including limits of detection, environmental background levels and regulatory cleanup levels should be fully considered in the enactment of remediation standards.
Netrin-1 Promotes Glioblastoma Cell Invasiveness and Angiogenesis by Multiple Pathways Including Activation of RhoA, Cathepsin B, and cAMP-response Element-binding Protein (2012)

Glioblastomas are very difficult tumors to treat because they are highly invasive and disseminate within the normal brain, resulting in newly growing tumors. We have identified netrin-1 as a molecule that promotes glioblastoma invasiveness. As evidence, netrin-1 stimulates glioblastoma cell invasion directly through Matrigel-coated transwells, promotes tumor cell sprouting and enhances metastasis to lymph nodes in vivo. Furthermore, netrin-1 regulates angiogenesis as shown in specific angiogenesis assays such as enhanced capillary endothelial cells (EC) sprouting and by increased EC infiltration into Matrigel plugs in vivo, as does VEGF-A. This netrin-1 signaling pathway in glioblastoma cells includes activation of RhoA and cyclic AMP response element-binding protein (CREB). A novel finding is that netrin-1-induced glioblastoma invasiveness and angiogenesis are mediated by activated cathepsin B (CatB), a cysteine protease that translocates to the cell surface as an active enzyme and co-localizes with cell surface annexin A2 (ANXA2). The specific CatB inhibitor CA-074Me inhibits netrin-1-induced cell invasion, sprouting, and Matrigel plug angiogenesis. Silencing of CREB suppresses netrin-1-induced glioblastoma cell invasion, sprouting, and CatB expression. It is concluded that netrin-1 plays an important dual role in glioblastoma progression by promoting both glioblastoma cell invasiveness and angiogenesis in a RhoA-, CREB-, and CatB-dependent manner. Targeting netrin-1 pathways may be a promising strategy for brain cancer therapy.