Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational design of a homotrimeric metalloprotein with a trisbipyridyl core

Significance This article reports the computational design of a threefold symmetric, self-assembling protein homotrimer containing a highly stable noncanonical amino acid-mediated metal complex within the protein interface. To achieve this result, recently developed protein–protein interface design methods were extended to include a metal-chelating noncanonical amino acid containing a bipyridine functional group in the design process. Bipyridine metal complexes can give rise to photochemical properties that would be impossible to achieve with naturally occurring amino acids alone, suggesting that the methods reported here could be used to generate novel photoactive proteins. Metal-chelating heteroaryl small molecules have found widespread use as building blocks for coordination-driven, self-assembling nanostructures. The metal-chelating noncanonical amino acid (2,2′-bipyridin-5yl)alanine (Bpy-ala) could, in principle, be used to nucleate specific metalloprotein assemblies if introduced into proteins such that one assembly had much lower free energy than all alternatives. Here we describe the use of the Rosetta computational methodology to design a self-assembling homotrimeric protein with [Fe(Bpy-ala)3]2+ complexes at the interface between monomers. X-ray crystallographic analysis of the homotrimer showed that the design process had near-atomic-level accuracy: The all-atom rmsd between the design model and crystal structure for the residues at the protein interface is ∼1.4 Å. These results demonstrate that computational protein design together with genetically encoded noncanonical amino acids can be used to drive formation of precisely specified metal-mediated protein assemblies that could find use in a wide range of photophysical applications.
Local Strain Measurement within Tendon

Abstract: Tendon is a dense connective tissue, responsible for transmitting the forces generated by muscles to the skeleton. It is composed of a hierarchical arrangement of crimped collagen fibres, interspersed with proteoglycan matrix and cells, known as tenocytes. During physiological loading, tendons are subjected to strains in the region of 5–6%, which result in the straightening and realignment of the collagen fibres, generating variable local strain fields within the tendon. This study demonstrates a technique for analysing local strains within viable tendon explants, during both loading and unloading of the tissue. Samples were strained in a custom‐designed rig, allowing real‐time visualisation of cell nuclei, used as local discrete markers, on a confocal microscope. Results indicated that local strains within the fascicle are smaller than the applied strains, never exceeding 1.2%, even at 8% gross applied strain. By contrast, the sliding of adjacent collagen units was recorded at each strain increment in this study, reaching a mean maximum of 3.9% of the applied displacement. Loading–unloading studies indicated that sliding behaviour is reversible up to strains of 5%, and provides the major extension mechanism within the rat‐tail tendon. This technique can be extended to further analyse shearing behaviour within the matrix.
Caspase-2 Short Isoform Interacts with Membrane-Associated Cytoskeleton Proteins to Inhibit Apoptosis

Caspase-2 (casp-2) is the most conserved caspase across species, and is one of the initiator caspases activated by various stimuli. The casp-2 gene produces several alternative splicing isoforms. It is believed that the long isoform, casp-2L, promotes apoptosis, whereas the short isoform, casp-2S, inhibits apoptosis. The actual effect of casp-2S on apoptosis is still controversial, however, and the underlying mechanism for casp-2S-mediated apoptosis inhibition is unclear. Here, we analyzed the effects of casp-2S on DNA damage induced apoptosis through “gain-of-function” and “loss-of-function” strategies in ovarian cancer cell lines. We clearly demonstrated that the over-expression of casp-2S inhibited, and the knockdown of casp-2S promoted, the cisplatin-induced apoptosis of ovarian cancer cells. To explore the mechanism by which casp-2S mediates apoptosis inhibition, we analyzed the proteins which interact with casp-2S in cells by using immunoprecipitation (IP) and mass spectrometry. We have identified two cytoskeleton proteins, Fodrin and α-Actinin 4, which interact with FLAG-tagged casp-2S in HeLa cells and confirmed this interaction through reciprocal IP. We further demonstrated that casp-2S (i) is responsible for inhibiting DNA damage-induced cytoplasmic Fodrin cleavage independent of cellular p53 status, and (ii) prevents cisplatin-induced membrane blebbing. Taken together, our data suggests that casp-2S affects cellular apoptosis through its interaction with membrane-associated cytoskeletal Fodrin protein.
Evaluation of Fungal Flora and Mycotoxin in Some Important Nut Products in Erbil Local Markets

In this study a wide range of moulds representing several genera and species was recorded. Ten samples of each pure and salted (almond, cashewnut, hazelnut, Peanut and pistachio) were collected from different markets (Shekhalla, Tayrawa and Qaysari) in Erbil city, Iraq. High infection of fungal genera was found in pure samples, while low infection was found in salted nut products samples, application of nuts with salts was found to increase the resistance of nuts to invasion and colonization by the fungi during storage. The total counts of fungi were 138×10 3 cfu/g. Samples by dilution method and represented twelve genera and twenty species of fungi by all method. Detection of Mycotoxin on Dichloran Rose Bengal Chloramphincol Agar (DRBC) for fungal isolation from nut samples showed, A. flavus, A. fumigatus, A. niger and A. ochraceous, positive results on the culture for mycotoxin production, change in colony diameter and color change in compare with control Czapek Dox Agar (CDA). Estimation of natural occurrence of Aflatoxin (AT) and Ochratoxin (OT) in nut product samples by using ELISA method, the results show low AF and OT content in most samples which is lower than the normal rang for human consumption. The high results of aflatoxin and ochratoxin show in peanut while the low results show in cashewnut.
Kerr-lens mode-locked bidirectional dual-comb ring laser for broadband dual-comb spectroscopy

Fourier-transform spectroscopy is an indispensable tool for analyzing chemical samples in scientific research as well as the chemical and pharmaceutical industries. Recently, its measurement speed, sensitivity, and precision have been shown to be significantly enhanced by using dual-frequency combs. Moreover, recent demonstrations of inducing nonlinear effects with ultrashort pulses have enriched the utility of dual-comb spectroscopy. However, wide acceptance of this technique is hindered by its requirement for two frequency combs and active stabilization of the combs. Here, we overcome this predicament with a Kerr-lens mode-locked bidirectional ring femtosecond-pulse laser that generates two broadband frequency combs with slightly different pulse repetition rates and a tunable yet highly stable rate difference. Since these combs are produced by one and the same laser cavity, their relative coherence stays passively stable without the need for active stabilization. To show its utility, we demonstrate broadband dual-comb spectroscopy with the single laser.
III–V compound semiconductor transistors—from planar to nanowire structures

Conventional silicon transistor scaling is fast approaching its limits. An extension of the logic device roadmap to further improve future performance increases of integrated circuits is required to propel the electronics industry. Attention is turning to III–V compound semiconductors that are well positioned to replace silicon as the base material in logic switching devices. Their outstanding electron transport properties and the possibility to tune heterostructures provide tremendous opportunities to engineer novel nanometer-scale logic transistors. The scaling constraints require an evolution from planar III–V metal oxide semiconductor field-effect transistors (MOSFETs) toward transistor channels with a three-dimensional structure, such as nanowire FETs, to achieve future performance needs for complementary metal oxide semiconductor (CMOS) nodes beyond 10 nm. Further device innovations are required to increase energy efficiency. This could be addressed by tunnel FETs (TFETs), which rely on interband tunneling and thus require advanced III–V heterostructures for optimized performance. This article describes the challenges and recent progress toward the development of III–V MOSFETs and heterostructure TFETs—from planar to nanowire devices—integrated on a silicon platform to make these technologies suitable for future CMOS applications.
Association between Serum Parathyroid Hormone Levels and the Prevalence of Atrial Fibrillation: the Dong-gu Study

Background and Objectives We aimed to investigate the association between serum parathyroid hormone (PTH) levels and the prevalence of atrial fibrillation (AF) in a population based study. Methods This study included a total of 9,007 community-dwelling Koreans aged 50 years and over who were enrolled in the Dong-gu study from 2007 to 2010. Electrocardiograms were recorded from the subjects using the HP-PageWriter 200 M1771A. All potential cases of AF were determined by 2 cardiologists. PTH concentration was measured by a chemiluminescent microparticle immunoassay. Multiple logistic regression analysis was used to evaluate the relationship between the quartiles of PTH and AF, adjusting for potential confounders. Results The prevalence of AF was 2.41% in males and 0.9% in females and increased with advanced age in both genders. The median and interquartile range (IQR) of serum PTH was 39.5 pg/mL (IQR, 30.6–50.8), which was significantly higher in patients with AF than in patients without AF (p<0.001). The prevalence of AF increased with increasing PTH quartile (0.8%, 0.9%, 1.6%, and 2.8% in the lowest, second, third, and highest PTH quartiles, respectively; p<0.001). Multivariable logistic analysis adjusted for cardiovascular risk factors showed the highest quartile of serum PTH levels was associated with a higher prevalence of AF than the lowest quartile (odds ratio, 3.34; 95% confidence interval, 1.93–5.78). Conclusions Higher levels of serum PTH were associated with higher prevalence of AF. Further studies are needed to determine whether this association is present in other populations and in a prospective study setting.
Implementation of power estimation methodology for intellectual property at SoC level

In VLSI design flow, the designer has better control over critical parameters such as power consumption and delay at higher levels of abstraction. Trade-offs and design changes are easier to accomplish at architectural and system levels. The decisions taken at these levels have a large impact on the final quality of the design. Power consumption has become a vital issue in all modern designs. However, actual information on this important metric is available only after the back-end phase when the design is committed to silicon. At this juncture, very little can be done to optimize power. Therefore, power estimation at higher levels is an extremely crucial step in executing power aware designs. Power estimation techniques can be applied at all abstraction levels in the low power design flow, of which highest level is system level. The design process at higher abstraction level shields the designer's crucial time and effort in power estimation. It is challenging to extract and analyse knowledge about the circuit of the system at the system level. If we estimate the power at this level, large power savings can be done and also power optimized design changes can be done. This paper describes an augmented power estimation methodology for intellectual property (IP) components. The method uses statistical methods to isolate a set of input influencing the output power for a particular mode of operation. The power model is developed as a function of parameters such as signal probability, transition density and spatial correlation. The proposed method was evaluated on a SDRAM controller core. The power estimation error varies from 0.3% to 12.5%.
Star-fish : Starfields + Fisheye Visualization and its Application to Federated Digital Libraries

We present star-fish, a focus+context approach to visualizing federations of large repositories that is based on the notion of starfields and is enhanced by functionality that allows users to keep track of the context of objects of their interest. This is accomplished through successive refinements of starfield representations in which areas of interest are magnified whereas surrounding areas are minimized, in the way of fisheye views. The resulting interface also makes use of iconic representations in starfields for differing types of collections, as well as colored variants for representing the institutions that hold the collections. The approach has been implemented on top a federation of digital libraries enabled by the OAI-PMH protocol.
Remote Ischemic Conditioning in Cardiovascular Surgery

The existing clinical studies on remote ischemic preconditioning in patients undergoing cardiovascular surgery are critically reviewed, with a focus on infarct size reduction and clinical outcome as end points. Confounders, notably the use of propofol anesthesia are identified. The need for better designed trials with a more targeted approach is emphasized.
2017 Energy-Efﬁcient Resource Allocation for Cache-Assisted Mobile Edge Computing

— In this paper, we jointly consider communication, caching and computation in a multi-user cache-assisted mobile edge computing (MEC) system, consisting of one base station (BS) of caching and computing capabilities and multiple users with computation-intensive and latency-sensitive applications. We propose a joint caching and ofﬂoading mechanism which involves task uploading and executing for tasks with uncached computation results as well as computation result downloading for all tasks at the BS, and efﬁciently utilizes multi-user diversity and multicasting opportunities. Then, we formulate the average total energy minimization problem subject to the caching and deadline constraints to optimally allocate the storage resource at the BS for caching computation results as well as the uploading and downloading time durations. The problem is a challenging mixed discrete-continuous optimization problem. We show that strong duality holds, and obtain an optimal solution using a dual method. To reduce the computational complexity, we further propose a low-complexity suboptimal solution. Finally, numerical results show that the proposed suboptimal solution outperforms existing comparison schemes.
A Two-Wired Ultra-High Input Impedance Active Electrode

This paper presents a novel two-wired active electrode that achieves ultrahigh input impedance using power supply bootstrapping. The proposed circuit reduces the input capacitance of a buffer amplifier while enabling measurements using leads with only two wires, providing a low-complexity and low-cost solution for interference rejection and artifact reduction in dc-coupled dry-contact biopotential measurements. An implemented prototype shows that, even using standard operational amplifiers, an input capacitance as low as 71 fF can be obtained, maintaining a high impedance in a 0–1 kHz bandwidth, sufficient for ECG, EEG, and EMG measurements. The circuit has a simple and easily replicable implementation that requires no individual adjustment. A common mode rejection ratio (CMRR) above 103 dB at 50 Hz was achieved and the increased rejection to interference due to the potential divider effect was experimentally tested maintaining a 92-dB CMRR at 50 Hz with a 1.2-M $\Omega$ source impedance unbalance. ECG measurements were conducted to validate the active electrode against a traditional alternative, and a test with dry-contact EEG electrodes was successfully conducted. Although the proposed circuit is intended to acquire superficial electrophysiological signals using dry electrodes, it can be used for measurement from other high-impedance sources, such as micropipette electrodes.
Fine Particulate Air Pollution and Hospital Emergency Room Visits for Respiratory Disease in Urban Areas in Beijing, China, in 2013

Background Heavy fine particulate matter (PM2.5) air pollution occurs frequently in China. However, epidemiological research on the association between short-term exposure to PM2.5 pollution and respiratory disease morbidity is still limited. This study aimed to explore the association between PM2.5 pollution and hospital emergency room visits (ERV) for total and cause-specific respiratory diseases in urban areas in Beijing. Methods Daily counts of respiratory ERV from Jan 1 to Dec 31, 2013, were obtained from ten general hospitals located in urban areas in Beijing. Concurrently, data on PM2.5 were collected from the Beijing Environmental Protection Bureau, including 17 ambient air quality monitoring stations. A generalized-additive model was used to explore the respiratory effects of PM2.5, after controlling for confounding variables. Subgroup analyses were also conducted by age and gender. Results A total of 92,464 respiratory emergency visits were recorded during the study period. The mean daily PM2.5 concentration was 102.1±73.6 μg/m3. Every 10 μg/m3 increase in PM2.5 concentration at lag0 was associated with an increase in ERV, as follows: 0.23% for total respiratory disease (95% confidence interval [CI]: 0.11%-0.34%), 0.19% for upper respiratory tract infection (URTI) (95%CI: 0.04%-0.35%), 0.34% for lower respiratory tract infection (LRTI) (95%CI: 0.14%-0.53%) and 1.46% for acute exacerbation of chronic obstructive pulmonary disease (AECOPD) (95%CI: 0.13%-2.79%). The strongest association was identified between AECOPD and PM2.5 concentration at lag0-3 (3.15%, 95%CI: 1.39%-4.91%). The estimated effects were robust after adjusting for SO2, O3, CO and NO2. Females and people 60 years of age and older demonstrated a higher risk of respiratory disease after PM2.5 exposure. Conclusion PM2.5 was significantly associated with respiratory ERV, particularly for URTI, LRTI and AECOPD in Beijing. The susceptibility to PM2.5 pollution varied by gender and age.
Investigation of the attenuation factor of Elekta carbon fiber table and its consistency in every direction

Objective:To investigate the dose influence of the latest full carbon fiber table in radiotherapy.Methods:We measured the attenuation factor o the latest full carbon fiber table and extended table plate using 0.6 cm3 ionization chamber.Results:The dose influence of treatment table increase with incidence angle increases.The attenuation factor for 6,10 and 15MVX on 60 degrees was 5.57,5.35 and 4.99 re-spectively;while on 300 degrees was 5.48,5.2 and 5.12 respectively.Conclusion:Latest full carbon fiber table influenced over radiation treatment dose of patients,with the oblique incident angle to increase,their influence showed increasing trend.The attenuation factor of treatment table could influence the dose to the target and its dose distribution.So the attenuation factor should be considered when the treatment plan-ning was designed in treatment planning system.
Application of Electronic Algorithms to Improve Diagnostic Evaluation for Bladder Cancer

Summary Background: Strategies to ensure timely diagnostic evaluation of hematuria are needed to reduce delays in bladder cancer diagnosis. Objective: To evaluate the performance of electronic trigger algorithms to detect delays in hematuria follow-up. Methods: We developed a computerized trigger to detect delayed follow-up action on a urinalysis result with high-grade hematuria (>50 red blood cells/high powered field). The trigger scanned clinical data within a Department of Veterans Affairs (VA) national data repository to identify all patient records with hematuria, then excluded those where follow-up was unnecessary (e.g., terminal illness) or where typical follow-up action was detected (e.g., cystoscopy). We manually reviewed a randomly-selected sample of flagged records to confirm delays. We performed a similar analysis of records with hematuria that were marked as not delayed (non-triggered). We used review findings to calculate trigger performance. Results: Of 310,331 patients seen between 1/1/2012-12/31/2014, the trigger identified 5,857 patients who experienced high-grade hematuria, of which 495 experienced a delay. On manual review of 400 randomly-selected triggered records and 100 non-triggered records, the trigger achieved positive and negative predictive values of 58% and 97%, respectively. Conclusions: Triggers offer a promising method to detect delays in care of patients with high-grade hematuria and warrant further evaluation in clinical practice as a means to reduce delays in bladder cancer diagnosis.
Vegetarian diets and cardiovascular risk factors in black members of the Adventist Health Study-2

Abstract Objective To compare cardiovascular risk factors between vegetarians and non-vegetarians in black individuals living in the USA. Design A cross-sectional analysis of a sub-set of 592 black women and men enrolled in the Adventist Health Study-2 (AHS-2) cohort of Seventh-day Adventists. Setting Members of the AHS-2 cohort, who lived in all states of the USA and provinces of Canada. Subjects Black/African-American members of two sub-studies of AHS-2 where blood and physiological measurements were obtained. Results Of these women and men, 25 % were either vegan or lacto-ovo-vegetarians (labelled ‘vegetarian/vegans’), 13 % were pesco-vegetarian and 62 % were non-vegetarian. Compared with non-vegetarians, the vegetarian/vegans had odds ratios for hypertension, diabetes, high blood total cholesterol and high blood LDL-cholesterol of 0·56 (95 % CI 0·36, 0·87), 0·48 (95 % CI 0·24, 0·98), 0·42 (95 % CI 0·27, 0·65) and 0·54 (95 % CI 0·33, 0·89), respectively, when adjusted for age, gender, education, physical activity and sub-study. Corresponding odds ratios for obesity in vegetarian/vegans and pesco-vegetarians, compared with non-vegetarians, were 0·43 (95 % CI 0·28, 0·67) and 0·47 (95 % CI 0·27, 0·81), respectively; and for abdominal obesity 0·54 (95 % CI 0·36, 0·82) and 0·50 (95 % CI 0·29, 0·84), respectively. Results for pesco-vegetarians did not differ significantly from those of non-vegetarians for other variables. Further adjustment for BMI suggested that BMI acts as an intermediary variable between diet and both hypertension and diabetes. Conclusions As with non-blacks, these results suggest that there are sizeable advantages to a vegetarian diet in black individuals also, although a cross-sectional analysis cannot conclusively establish cause.