Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA sequence modulates the conformation of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme.

The conformations of C8-dG adducts of 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) positioned in the C-X1-G, G-X2-C, and C-X3-C contexts in the C-G1-G2-C-G3-C-C recognition sequence of the NarI restriction enzyme were compared, using the oligodeoxynucleotides 5'-d(CTCXGCGCCATC)-3'. 5'-d(GATGGCGCCGAG)-3', 5'-d(CTCGXCGCCATC)-3'. 5'-d(GATGGCGCCGAG)-3', and 5'-d(CTCGGCXCCATC)-3'. 5'-d(GATGGCGCCGAG)-3' (X is the C8-dG adduct of IQ). These were the NarIIQ1, NarIIQ2, and NarIIQ3 duplexes, respectively. In each instance, the glycosyl torsion angle chi for the IQ-modified dG was in the syn conformation. The orientations of the IQ moieties were dependent upon the conformations of torsion angles alpha' [N9-C8-N(IQ)-C2(IQ)] and beta' [C8-N(IQ)-C2(IQ)-N3(IQ)], which were monitored by the patterns of 1H NOEs between the IQ moieties and the DNA in the three sequence contexts. The conformational states of IQ torsion angles alpha' and beta' were predicted from the refined structures of the three adducts obtained from restrained molecular dynamics calculations, utilizing simulated annealing protocols. For the NarIIQ1 and NarIIQ2 duplexes, the alpha' torsion angles were predicted to be -176 +/- 8 degrees and -160 +/- 8 degrees , respectively, whereas for the NarIIQ3 duplex, torsion angle alpha' was predicted to be 159 +/- 7 degrees . Likewise, for the NarIIQ1 and NarIIQ2 duplexes, the beta' torsion angles were predicted to be -152 +/- 8 degrees and -164 +/- 7 degrees , respectively, whereas for the NarIIQ3 duplex, torsion angle beta' was predicted to be -23 +/- 8 degrees . Consequently, the conformations of the IQ adduct in the NarIIQ1 and NarIIQ2 duplexes were similar, with the IQ methyl protons and IQ H4 and H5 protons facing outward in the minor groove, whereas in the NarIIQ3 duplex, the IQ methyl protons and the IQ H4 and H5 protons faced into the DNA duplex, facilitating the base-displaced intercalated orientation of the IQ moiety [Wang, F. , Elmquist, C. E. , Stover, J. S. , Rizzo, C. J., and Stone, M. P. (2006) J. Am. Chem. Soc. 128, 10085-10095]. In contrast, for the NarIIQ1 and NarIIQ2 duplexes, the IQ moiety remained in the minor groove. These sequence-dependent differences suggest that base-displaced intercalation of the IQ adduct is favored when both the 5'- and 3'-flanking nucleotides in the complementary strand are guanines. These conformational differences may correlate with sequence-dependent differences in translesion replication.
A Comparison of the Composite International Diagnostic Interview (CIDI-Auto) with Clinical Assessment in Diagnosing Mood and Anxiety Disorders

Objective: Increasingly, epidemiological studies are employing computerized and highly standardized interviews, such as the Composite International Diagnostic Interview (CIDIAuto), to assess the prevalence of psychiatric illness. Recent studies conducted in specialist units have reported poor agreement between experienced clinicians’ and CIDI-Auto diagnoses. In this study we investigated the concordance rate between clinicians and the CIDI-Auto for the diagnosis of six anxiety disorders and two mood disorders, whereby the CIDI-Auto was treated as the ‘gold standard’. Method: Subjects were 262 patients who were assessed by a clinical psychologist or psychiatrist and completed the CIDI-Auto at a tertiary referral unit for anxiety and mood disorders. Agreement between the clinicians’ diagnoses and the diagnoses generated by the CIDI-Auto according to both DSM-IV and ICD-10 codes, were examined by kappa statistics. Sensitivity and specificity values were also calculated. Results: Agreement between clinicians and the CIDI-Auto (DSM-IV) ranged from poor for social phobia and posttraumatic stress disorder (κ < 0.30) to moderate for obsessive– compulsive disorder (OCD; κ = 0.52). Agreement between clinicians and the CIDI-Auto (ICD-10) ranged from poor for major depressive episode (κ = 0.25) to moderate for OCD (κ = 0.57). With the CIDI diagnosis treated as the gold standard, clinicians’ diagnoses showed low sensitivity (κ < 0.70) for all the disorders except for OCD (for ICD-10), but high specificity (κ < 0.70) for all the disorders. Conclusion: Poor agreements between experienced clinicians and the CIDI-Auto were reported for anxiety and mood disorders in the current study. A major implication is that if diagnosis alone directed treatment, then patients could receive different treatments, depending on whether the computer, or a clinician, made the diagnosis.
3.3F catheter/sheath system for use in diagnostic neuroangiography.

BACKGROUND AND PURPOSE Although neuroangiography remains the criterion standard standard for the detection of and surgical/interventional planning for cerebrovascular diseases, it usually requires that patients be confined to bed rest for several hours after angiography to prevent local complications. Decreasing catheter size has reduced the risk of hemorrhagic complications associated with early ambulation after angiography. For this study, we prospectively evaluated the clinical feasibility of a 3.3F catheter/sheath system for selective neuroangiography. METHODS One hundred seventeen consecutive patients (49 men, 68 women; age range, 18-83 years; mean age, 56.9 years) underwent selective neuroangiography using 3.3F catheters. The exclusion criteria for this study included a subsequent surgical/neurointerventional procedure performed within 18 hours and necessity of arch aortography, which is routinely performed for the first examination of patients with ischemic cerebrovascular diseases. The procedure was evaluated prospectively in terms of success rate, compression time of the arterial puncture site, and periprocedural complications. RESULTS Selective catheterization of the intended arteries was performed in 99% of the carotid arteries and 97.4% of the vertebral arteries. No neurologic complications or local hemorrhagic complications were observed. Manual compression time after the procedure ranged from 3 to 7 minutes (mean, 3.7 minutes), and patient bed rest after the procedure ranged from 2 to 3 hours (mean, 2.04 hours). CONCLUSION Selective neuroangiography with a 3.3F catheter/sheath system is feasible and enables early ambulation in selected patients.
Factors Governing Sustainable Groundwater Pumping near a River

The objective of this paper was to provide new insights into processes affecting riverbank filtration (RBF). We consider a system with an inflatable dam installed for enhancing water production from downstream collector wells. Using a numerical model, we investigate the impact of groundwater pumping and dam operation on the hydrodynamics in the aquifer and water production. We focus our study on two processes that potentially limit water production of an RBF system: the development of an unsaturated zone and riverbed clogging. We quantify river clogging by calibrating a time‐dependent riverbed permeability function based on knowledge of pumping rate, river stage, and temperature. The dynamics of the estimated riverbed permeability reflects clogging and scouring mechanisms. Our results indicate that (1) riverbed permeability is the dominant factor affecting infiltration needed for sustainable RBF production; (2) dam operation can influence pumping efficiency and prevent the development of an unsaturated zone beneath the riverbed only under conditions of sufficient riverbed permeability; (3) slow river velocity, caused by dam raising during summer months, may lead to sedimentation and deposition of fine‐grained material within the riverbed, which may clog the riverbed, limiting recharge to the collector wells and contributing to the development of an unsaturated zone beneath the riverbed; and (4) higher river flow velocities, caused by dam lowering during winter storms, scour the riverbed and thus increase its permeability. These insights can be used as the basis for developing sustainable water management of a RBF system.
Improve Web Search Ranking by Co-ranking SVM

Learning to rank technique is attacking much attention in search engine optimization. However, it cost a lot to collect labeled data for rank learning. In addition, the features of learning better ranking functions, such as click-through features and social annotation features, proposed from different viewpoints. In this paper, we propose to consider the learning to rank problem in the co-training framework, which can gather information from different types of features and incorporate unlabeled data into training. A bottleneck of considering rank learning in co-training framework is that the single view Web features always fail to give accurate ranking results due to their limitations in real tasks. For instances, sparseness of social annotation and the bias of user click-through may make them fail. To solve this bottleneck, we propose a feature fusion algorithm that enables the features from different views to enhance each other before co-training. Though the independencies assumption might be violated due to feature fusion, we introduce a sample selection strategy which guarantees co-training to work effectively. Experimental results on real search log and social annotations show that our proposed method can effectively improve the ranking performance by utilizing our feature fusion and sample selection strategies.
Meta-analysis of a possible signal of increased mortality associated with cefepime use.

BACKGROUND On the basis of meta-analyses, concern has been raised regarding a possible signal of increased mortality associated with the use of cefepime versus other beta-lactam antibiotics. To further investigate this possible signal, we accessed findings and data from published and unpublished cefepime clinical trials. METHODS We performed meta-analyses using trial- and patient-level data from comparative trials. Trial-level analyses were performed using summary data from all patients in the trials, and patient-level analyses were performed on trials for which patient-level data were available. Thirty-day, all-cause mortality was analyzed using the Mantel-Haenszel adjusted risk difference (ARD) method. RESULTS The trial-level meta-analysis was based on 88 trials (9467 cefepime patients and 8288 comparator patients). The 30-day, all-cause mortality rates were 6.21% (588/9467) for the cefepime patients and 6.00% (497/8288) for comparator patients (ARD per 1000 population, 5.38; 95% confidence interval [CI], -1.53 to 12.28). In the patient-level analysis (35 trials, 5058 cefepime patients, and 3976 comparator patients), 30-day, all-cause mortality rates were 5.63% (285/5058) for cefepime patients and 5.68% (226/3976) for comparator patients (ARD per 1000 population, 4.83; 95% CI, -4.72 to 14.38). A sensitivity analysis based solely on the 24 febrile neutropenia trials did not show a statistically significant increase in mortality with cefepime use (ARD per 1000 population, 9.67; 95% CI, -2.87 to 22.21). CONCLUSIONS In both trial-level and patient-level meta-analyses, we did not identify a statistically significant increase in mortality among cefepime-treated patients, compared with those treated with other antibacterials.
Instrument-driven constrains on scattering modeling for TerraSAR-X POLSAR data

This paper shows the necessity to include the impact of instrument-driven constrains in the physical modeling of polarimetric data from spaceborne SAR missions, specifically for TerraSAR-X (TSX) case. The intrinsic acquisition of fully (quad-pol) polarimetric data, exploiting the dual-receive antenna (DRA) mode, may induce two additional sources of decorrelation when observing challenging dynamic scenarios, such as the ocean or sea: limited signal-to-noise ratio (SNR) as the receive antenna is halved and temporal decor-relation induced over the along-track configuration (spatial baseline between the polarimetic channels) due to internal clutter motion. Experimental quad-pol TSX data over the ocean has been used to study the applicability of the original X-Bragg model as well as its extension accounting for these system/scenario dependent limitations, which shows a much better fitting.
Naringin suppresses the development of glioblastoma by inhibiting FAK activity

Abstract As the most common and lethal primary malignant brain cancer, glioblastoma is hard to timely diagnose and sensitive therapeutic monitoring. It is essential to develop new and effective drugs for glioblastoma multiform. Naringin belongs to citrus flavonoids and was found to display strong anti-inflammatory, antioxidant and antitumor activities. In this report, we found that naringin can specifically inhibit the kinase activity of FAK and suppress the FAKp-Try397and its downstream pathway in glioblastoma cells. Our study showed out that naringin can inhibit cell proliferation by inhibiting FAK/cyclin D1 pathway, promote cell apoptosis through influencing FAK/bads pathway, at the same time, it can also inhibit cell invasion and metastasis by inhibiting the FAK/mmps pathway. All these showed that naringin exerts the anti-tumor effects in U87 MG by inhibiting the kinase activity of FAK.
Internationalisation of Higher Education: Proposed Framework on International Students' Satisfaction

There are many dimensions in the internationalisation of higher education. One of the dimensions is international students. This dimension has been given great emphasis by many institutions for diverse reasons such as economy, while others are reputation and ranking of the university. Universities around the globe undergo tremendous pressure due to stiff competition both in terms of student enrolment and securing fund. All these have posed a great challenge to universities to re-look into improving services and quality to attract international students. Hence, universities need to carefully analyse key factors contributing to international students’ satisfaction by developing strategies accordingly. Institutions need to provide quality service and environment for international students to ensure that they are satisfied with the services received while pursing their studies. Students who are satisfied will help to attract more potential students to the institutions through increased student loyalty, positive word of mouth (WOM) communication and image of the higher education institutions (Arambewela, 2003; Arambewela & Hall, 2006). Based on the literature review, this paper aims to present various factors contributing to international students’ satisfaction. These factors are translated into variables to measure international students’ satisfaction, which can be used as a guideline by higher education institutions.
Cell‐surface Metalloprotease ADAM12 is Internalized by a Clathrin‐ and Grb2‐dependent Mechanism

ADAM12 (A Disintegrin And Metalloprotease 12), a member of the ADAMs family of transmembrane proteins, is involved in ectodomain shedding, cell‐adhesion and signaling, with important implications in cancer. Therefore, mechanisms that regulate the levels and activity of ADAM12 at the cell‐surface are possibly crucial in these contexts. We here investigated internalization and subsequent recycling or degradation of ADAM12 as a potentially important regulatory mechanism. Our results show that ADAM12 is constitutively internalized primarily via the clathrin‐dependent pathway and is subsequently detected in both early and recycling endosomes. The protease activity of ADAM12 does not influence this internalization mechanism. Analysis of essential elements for internalization established that proline‐rich regions in the cytoplasmic domain of ADAM12, previously shown to interact with Src‐homology 3 domains, were necessary for proper internalization. These sites in the ADAM12 cytoplasmic domain interacted with the adaptor protein growth factor receptor‐bound protein 2 (Grb2) and knockdown of Grb2 markedly reduced ADAM12 internalization. These studies establish that internalization is indeed a mechanism that regulates ADAM cell surface levels and show that ADAM12 internalization involves the clathrin‐dependent pathway and Grb2.
An energy aware dynamic cluster head selection mechanism for wireless sensor networks

Energy efficiency in data collection and dissemination is a very important factor in wireless sensor networks. Therefore, minimizing energy consumption and maximizing network lifetime are the key factors for the design of wireless sensor network protocols. One of the energy conservation techniques is to select proper cluster head in a cluster. In this paper, a protocol has been proposed to select the sensor node as cluster head, in the sense that choosing the closest sensor node to low-energy nodes will result in lesser energy consumption and early death prevention of nodes. The simulation results have been shown that the proposed protocol could enhance the network lifetime.
The Influence of Rehabilitative and Punishment Ideology on Correctional Officers’ Perceptions of Informal Bases of Power

Maintaining order is a key goal for prison managers. Much of the research on order maintenance focuses, however, on disruptions of order, even when order is more common. Examining factors related to perceptions on how officers get inmates to comply is, therefore, an important consideration. Using a survey of correctional officers from a Mid-Atlantic state, this study considers three dimensions of French and Raven’s theory on the bases of power. The focus is to examine correctional orientation and compliance regarding three dimensions of power that rely on informal control and relationships. The results indicate that officers’ belief in rehabilitative ideals is consistently related to the dimensions of legitimate, referent, and expert control. Other individual and organizational factors are also related to dimensions of power. Implications for policies and for future research are discussed.
UoI-NMF Cluster: A Robust Nonnegative Matrix Factorization Algorithm for Improved Parts-Based Decomposition and Reconstruction of Noisy Data

With the ever growing collection of large volumes of scientific data, development of interpretable machine learning tools to analyze such data is becoming more important. However, robust, interpretable machine learning tools are lacking, threatening extraction of scientific insight and discovery. Nonnegative Matrix Factorization (NMF) algorithms decompose an m × n nonnegative data matrix A into a k × n basis matrix H and an m × k weight matrix W, such that A ≈ WH, where k is the desired rank. In this paper, we present a novel two stage algorithm, UoI-NMF_cluster for NMF, which is based on three innovations: (i) completely separate bases learning from weight estimation, (ii) learn bases by clustering NMF results across bootstrap resamples of the data, and (iii) use the recently introduced Union of Intersections (UoI) framework to estimate ultra-sparse weights that maximize data reconstruction accuracy. We deploy our algorithm on various synthetic and scientific data to illustrate its performance, with a focus on neuroscience data. Compared to other NMF algorithms, UoI-NMF_cluster yields: a) more accurate parts-based decompositions of noisy data, b) a sparse and accurate weight matrix, and c) high accuracy reconstructions of the de-noised data. Together, these improvements enhance the performance and interpretability of NMF application to noisy data, and suggest similar approaches may benefit other matrix decomposition algorithms.
HAR volatility modelling with jump

Heterogeneity and jump are two important factors influencing volatility. Ignoring heterogeneity and jump would reduce the quality of the realized volatility model. Underestimating downside risk is produced. In the present work we investigate the influence of heterogeneity and jump on volatility, establish a HAR-RV-J model based on the HAR-RV models. Our research demonstrates that the empirical results of HAR-RV-J model considering the jump effect presents better statistical indicators in the mainland stocks. Moreover, it is found that the forecasting performance of HAR-RV-J model is better than HAR-RV model by comparing RMSE, MAE and MAPE. It indicates that the combination of HAR-RV model and jump improves the estimation accuracy of the realized volatility in Chinese mainland stocks, which is more advantageous to the risk management of financial assets.
Effect of body position on measurements of diffusion capacity after exercise

Background—Pulmonary diffusing capacity for carbon monoxide (Dlco), alveolar capillary membrane diffusing capacity (Dm), and pulmonary capillary blood volume (Vc) are all significantly reduced after exercise. Objective—To investigate whether measurement position affects this impaired gas transfer. Methods—Before and one, two, and four hours after incremental cycle ergometer exercise to fatigue, single breath Dlco, Dm, and Vc measurements were obtained in 10 healthy men in a randomly assigned supine and upright seated position. Results—After exercise, Dlco, Dm, and Vc were significantly depressed compared with baseline in both positions. The supine position produced significantly higher values over time for Dlco (5.22 (0.13) v 4.66 (0.15) ml/min/mm Hg/l, p = 0.022) and Dm (6.78 (0.19) v 6.03 (0.19) ml/min/mm Hg/l, p = 0.016), but there was no significant position effect for Vc. There was a similar pattern of change over time for Dlco, Dm, and Vc in the two positions. Conclusions—The change in Dlco after exercise appears to be primarily due to a decrease in Vc. Although the mechanism for the reduction in Vc cannot be determined from these data, passive relocation of blood to the periphery as the result of gravity can be discounted, suggesting that active vasoconstriction of the pulmonary vasculature and/or peripheral vasodilatation is occurring after exercise.
Pathogenicity and Infection Cycle of Vibrio owensii in Larviculture of the Ornate Spiny Lobster (Panulirus ornatus)

ABSTRACT The type strain of Vibrio owensii (DY05) was isolated during an epizootic of aquaculture-reared larvae (phyllosomas) of the ornate spiny lobster (Panulirus ornatus). V. owensii DY05 was formally demonstrated to be the etiological agent of a disease causing rapid and reproducible larval mortality with pathologies similar to those seen during disease epizootics. Vectored challenge via the aquaculture live feed organism Artemia (brine shrimp) caused consistent cumulative mortality rates of 84 to 89% after 72 h, in contrast to variable mortality rates seen after immersion challenge. Histopathological examination of vector-challenged phyllosomas revealed bacterial proliferation in the midgut gland (hepatopancreas) concomitant with epithelial cell necrosis. A fluorescent-protein-labeled V. owensii DY05 transconjugant showed dispersal of single cells in the foregut and hepatopancreas 6 h postexposure, leading to colonization of the entire hepatopancreas within 18 h and eventually systemic infection. V. owensii DY05 is a marine enteropathogen highly virulent to P. ornatus phyllosoma that uses vector-mediated transmission and release from host association to a planktonic existence to perpetuate transfer. This understanding of the infection process will improve targeted biocontrol strategies and enhance the prospects of commercially viable larviculture for this valuable spiny lobster species.