Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid knot detection and application to protein structure prediction

MOTIVATION Knots in polypeptide chains have been found in very few proteins, and consequently should be generally avoided in protein structure prediction methods. Most effective structure prediction methods do not model the protein folding process itself, but rather seek only to correctly obtain the final native state. Consequently, the mechanisms that prevent knots from occurring in native proteins are not relevant to the modeling process, and as a result, knots can occur with significantly higher frequency in protein models. Here we describe Knotfind, a simple algorithm for knot detection that is fast enough for structure prediction, where tens or hundreds of thousands of conformations may be sampled during the course of a prediction. We have used this algorithm to characterize knots in large populations of model structures generated for targets in CASP 5 and CASP 6 using the Rosetta homology-based modeling method. RESULTS Analysis of CASP5 models suggested several possible avenues for introduction of knots into these models, and these insights were applied to structure prediction in CASP 6, resulting in a significant decrease in the proportion of knotted models generated. Additionally, using the knot detection algorithm on structures in the Protein Data Bank, a previously unreported deep trefoil knot was found in acetylornithine transcarbamylase. AVAILABILITY The Knotfind algorithm is available in the Rosetta structure prediction program at http://www.rosettacommons. org.
Controllability for pairs of vehicles maintaining constant distance

This paper studies the controllability of pairs of identical nonholonomic vehicles maintaining a constant distance. The study provides controllability results for the five most common types of robot vehicles: Dubins, Reeds-Shepp, differential drive, car-like and convexified Reeds-Shepp. The challenge of achieving controllability of such systems is that their admissible control domains depend on configuration variables. A theorem of controllability specifical for such systems has been obtained based on known controllability theorems. As a result, we show that pairs of the latter three types are completely controllable, i.e. can be steered between any two arbitrary configurations. The same does not hold for pairs of Dubins or Reeds-Shepp vehicles, and a description of the reachable sets in these cases is provided. Finally, as direct extension of controllability results of pairs of identical vehicles, the controllability results for two kinds of formation of n identical vehicles are presented.
Outcome of operable oral cavity cancer and impact of maintenance metronomic chemotherapy: A retrospective study from rural India

Abstract Background: Oral cavity cancer is the most common cancer among rural India. There is a paucity of data for outcomes of operable oral cavity cancer from rural India. Use of maintenance metronomic may delay or avoid relapse. Aim: To evaluate outcomes of operable oral cavity carcinoma and evaluate impact of maintenance metronomic chemotherapy. Objectives: To evaluate disease-free survival (DFS), overall survival (OS), and factors affecting the outcome in operable oral cavity cancer. Materials and Methods: Data of patients diagnosed with oral cavity cancer registered between May 2008 and May 2014 were retrieved. Only those patients with operable oral cavity cancer and upfront definitive surgery were included in the study. Demographic profile, stage, tobacco consumption, adjuvant therapy, and pattern of failure were collected. Kaplan-Meir survival analysis was used to determine DFS and OS. Log-rank test was used to evaluate factors affecting outcome. Results: Median follow-up is 24 months. Out of 335 patients, 225 (67%) had advanced operable cancer with 42/225 (18%) and 183/225 (82%) as Stages III and IVA, respectively. Buccal mucosa was the most common subsite (178/335, 53%) followed by tongue (63/335, 19%). Ninety-two percent patients were addicted to smokeless tobacco, whereas 27% were smokers. Median DFS is 13 months with 2 years relative DFS 32%. Median OS is 30 months, with 2 years OS of 54%. Metronomic adjuvant oral chemotherapy was given in 130/225 (58%); Stage III and IVA patients with median of 14 months (3-18 months). Use of metronomic chemotherapy improved DFS (8 vs. 14 months, P = 0.22) and OS (14 vs. 26 months, P = 0.04). Conclusion: Oral cavity cancer is a major health care problem in rural India. Presentation at advanced stage leads to suboptimal outcomes. Benefit of metronomic maintenance chemotherapy in locally advanced oral cavity needs to be further evaluated prospectively.
Learning Audio Features for Singer Identification and Embedding

There has been an increasing use of neural networks for music information retrieval tasks. In this paper, we empirically investigate different ways of improving the performance of convolutional neural networks (CNNs) on spectral audio features. More specifically, we explore three aspects of CNN design: depth of the network, the use of residual blocks along with the use of grouped convolution, and global aggregation over time. The application context is singer classification and singing performance embedding and we believe the conclusions extend to other types of music analysis using convolutional neural networks. The results show that global time aggregation helps to improve the performance of CNNs the most. Another contribution of this paper is the release of a singing recording dataset that can be used for training and evaluation.
Murmurs of thought: Phenomenology of hallucinatory consciousness in impending psychosis

First‐person accounts and detailed phenomenological descriptions are decisive to improve our understanding of auditory verbal hallucinations (AVHs). This is crucial in order to adequately appreciate the biographical–existential complexity of the “voices” and to increase the communication and share‐ability of such experiences. Besides the clear normalizing/de‐stigmatizing value, such an approach has an eminent therapeutic value since it offers a non‐reifying way to approach the broad, gestaltic metamorphosis of consciousness which precedes fully formed, florid AVHs. However, an important feature – namely, the very experiential genesis of the voices before their manifestation as full‐blown AVHs – has up to now not received sufficient attention. “Voices” indeed are often anticipated by subtle pre‐psychotic distortions of the stream of consciousness – such as abnormal sonorization of the inner dialogue and/or perceptualization of thought – which could emerge at the beginning of the prodromal phase. We suggest that a careful attention to these not‐yet psychotic precursors in their experiential continuity with AVHs could have important therapeutic implications.
Re-examining the social construction of ‘elder abuse and neglect’: A Canadian perspective

Many questions and contradictions pervade both the understanding of what has come to be known as ‘elder abuse and neglect’ and attempts to address it. Four major competing constructions reflecting four differing needs discourses can be discerned in legislation, programmes and services, and in the actions of individuals. In this paper these constructions are introduced, examined and situated, with reference to the social and historical antecedents that have contributed to the emergence of elder abuse and neglect as a social problem. The article considers how these constructions are manifest in public and private responses to elder abuse and neglect, through discussion of the Canadian experience of service delivery to older people in situations of mistreatment and neglect, in non-institutional settings. It is concluded that deeply embedded value conflicts in Canadian society and in its political economy, compound the problem of resolving issues of mistreatment through public policy.
Resolution Dependence of Magnetorotational Turbulence in the Isothermal Stratified Shearing Box

Magnetohydrodynamic turbulence driven by the magnetorotational instability can provide diffusive transport of angular momentum in astrophysical disks, and a widely studied computational model for this process is the ideal, stratified, isothermal shearing box. Here we report results of a convergence study of such boxes up to a resolution of N = 256 zones per scale height, performed on blue waters at NCSA with ramses-gpu. We find that the time and vertically integrated dimensionless shear stress , i.e., the shear stress is resolution dependent. We also find that the magnetic field correlation length decreases with resolution, . This variation is strongest at the disk midplane. We show that our measurements of are consistent with earlier studies, and we discuss possible reasons for the lack of convergence.
Performance analysis of compact antenna arrays with MRC in correlated Nakagami fading channels

This paper presents the average error probability performance of a compact space diversity receiver for the reception of binary coherent and noncoherent modulation signals through a correlated Nakagami (1960) fading channel. Analytical expressions of the average bit error rate (BER) are derived as a function of the covariance matrix of the multipath component signals at the antenna elements. Closed-form expressions for the spatial cross-correlation are obtained under a Gaussian angular power profile assumption, taking account of the mutual coupling between antenna elements. The effects of antenna array configuration (geometry and electromagnetic coupling) and the operating environment (fading, angular spread, mean angle-of-arrival) on the BER performance are illustrated.
Secure broadcasting of a common message with independent secret keys

The problem of secure broadcasting with independent secret keys is studied. The particular scenario is analyzed where a common message has to be broadcasted to two legitimate receivers, while keeping an external eavesdropper ignorant of it. The transmitter shares independent secret keys of arbitrary rates with both legitimate receivers, which can be used in different ways: They can be used as one-time pads to encrypt the common message or they can be used as randomization resources for wiretap coding. Both approaches are studied in this paper. If both legitimate channels are degraded versions of the eavesdropper channel, it is shown that the one-time pad approach is optimal for several cases yielding corresponding capacity expressions. Reversely, the wiretap coding approach is shown to be optimal if the eavesdropper channel is degraded with respect to both legitimate channels establishing capacity in this case as well.
Experimental study of advanced MU-MIMO scheme with antenna calibration for the evolving LTE TDD system

As the 3GPP long term evolution (LTE) system actively evolves, advanced multi-user multiple-input multiple-output (MU-MIMO) schemes have attracted increasing interest in the engineering field. We have proposed a QR decomposition (QRD) based MU-MIMO scheme for the evolving LTE time division duplex (TDD) system to achieve high spectrum efficiency, assuming ideal channel reciprocity. In order to investigate the promising performance of TDD MU-MIMO in practice, we implement the proposed QRD-based TDD MU-MIMO scheme together with an actual over-the-air (OTA) antenna calibration scheme into our FPGA-based hardware testbed for the evolving LTE TDD system to examine its performance under the constraint of practical channel reciprocity. Measurement results show that channel reciprocity indeed could be achieved with the OTA antenna calibration and the QRD-based MU-MIMO scheme can effectively make use of this channel reciprocity to achieve high spectrum efficiency data transmission for both downlink and uplink. Moreover, the influence of antenna calibration on the TDD MU-MIMO performance is further investigated and several considerations related to antenna calibration are addressed.
The role of contextual supports and barriers in the choice of math/science educational options: A test of social cognitive hypotheses

Social cognitive career theory proposes that contextual supports and barriers play key roles in the career choice process, yet little research has examined hypotheses involving these variables. Participants (111 1 college students) completed measures of math/science-related course self-efficacy, coping efficacy, outcome expectations, interests, goals, and perceived contextual supports and barriers. Findings indicate that self-efficacy and outcome expectations were jointly predictive of interests and choice intentions. Support and barrier percepts produced only weak direct relations to choice, though barrier percepts were found to moderate interest-choice relations. A model portraying barriers and supports as linked to choice indirectly (via their impact on self-efficacy) produced better fit to the data than did a model specifying barriers and supports as directly linked to choice. Implications for future research and counseling are discussed.
Invisible Disabilities and Employment Testing

Santuzzi, Waltz, Finkelstein, and Rupp (2014) present an interesting point of view on the topic of invisible disabilities, both from the employee’s perspective as well as the organization’s. However, there is an area of importance to industrial–organizational (I–O) psychology that was largely ignored in their review. For practitioners involved in the employment testing field (preemployment or otherwise), invisible disabilities pose a special challenge. For employment testing applications, most of the issues that Santuzzi et al. raise are spot on. At the same time, there are unique issues in the testing arena that should be raised in more detail. In this reply, it is argued that testing individuals with disabilities is a special area of ‘‘challenge’’ for I–O psychology, and some suggestions are outlined for advancing the field in that specialized area.
A Review of Strategies for Validating Computer-Automated Scoring

Computer-automated scoring (CAS) is becoming a popular tool in assessment. Various studies have been conducted to assess the quality of CAS-system-generated scores. There is then a need for a systematic examination of these studies in the context of contemporary validity concepts and current practice. This article starts with a brief introduction to current CAS systems. Next, we review the current practice of validating CAS-system-generated scores. Finally, we present a conceptual framework and general recommendations for designing validation studies for CAS procedures.
Helicobacter pylori Stimulates a Mixed Adaptive Immune Response with a Strong T‐Regulatory Component in Human Gastric Mucosa

Background: Host factors play an important role in the pathophysiology of Helicobacter pylori infection and development of gastritis and related disease. The established opinion is that the T‐cell‐mediated immune response to H. pylori infection is of Th1 type. Our earlier immune cell phenotype studies indicate a mixed Th1–Th2 profile of the effector cells. Therefore, an extensive adaptive and regulatory cytokine gene expression profile was conducted by quantitative real‐time polymerase chain reaction (qPCR).
Do Prices Determine Vertical Integration? Evidence from Trade Policy

What is the relationship between product prices and vertical integration? While the literature has focused on how integration affects prices, this paper shows that prices can affect integration. Many theories in organizational economics and industrial organization posit that integration, while costly, increases productivity. If true, it follows from firms' maximizing behavior that higher prices cause firms to choose more integration. The reason is that at low prices, increases in revenue resulting from enhanced productivity are too small to justify the cost, whereas at higher prices, the revenue benefit exceeds the cost. Trade policy provides a source of exogenous price variation to assess the validity of this prediction: higher tariffs should lead to higher prices and therefore to more integration. We construct firm-level indices of vertical integration for a large set of countries and industries and exploit cross-section and time-series variation in import tariffs to examine their impact on firm boundaries. Our empirical results provide strong support for the view that output prices are a key determinant of vertical integration.
Space-time coding for wireless channels with partial-band noise jammers

In this paper, we investigate the performance of space-time codes for wireless transmission with the occurrance of partial-band noise jammers. The maximum likelihood (ML) decoding is derived together with several low-complexity subop- timal schemes. The design criteria of good space-time codes are presented with respect to the wireless jamming channels. Verified by the simulation results, the proposed system outperforms the conventional schemes in terms of both signal-to-noise ratio and bandwidth efficiency.
Abdominal pain in a female infant: suspected intussusception.

This 6-month old female with a past medical history of colic/ formula intolerance presented to the emergency department with a 2-day history of nausea, vomiting, decreased oral intake, irritability, and lethargy. The mother also related that the infant would intermittently cry and flex her legs and hips. After a few seconds, she would relax, then begin crying and posturing again. These episodes had been increasing in frequency over the past 24 hours. The remainder of the history was unremarkable. On presentation to our emergency department, the patient was alert but fussy and on abdominal examination was tender to palpation, greater on the right. There was voluntary guarding but there were no palpable masses, and there was no rebound tenderness. The remainder of the physical examination was within normal limits except for mild dehydration. The patient was suspected of having intussusception and because of this an ultrasound study was performed. No intussusception was identified but rather, an oval, solid mass, measuring 4 cm 2 cm with discrete round cystic areas was discovered in the pelvis (Fig. 1). What do you make of this? FIGURE 1. Ultrasound study of the abdomen/pelvis. Radiology in the ED
The effect of ‘risk-thinking’ on the contemporary construction of teenage motherhood

In Britain over the past 12 years, despite the normalising of sex and reproduction outside marriage, and contrary to the evidence that there are fewer teenage parents than in the past, teenage parenthood has become amplified as a social problem. The existence of such a paradox suggests that this problematisation has captured a number of significant political and social dynamics and anxieties, in particular, the co-existence of widespread concern with social disorder and moral decline with the recognition that past forms of social and moral ordering have an alienating rather than a cohering effect. This paper explores: how the problem of teenage pregnancy has been both amplified and redefined; the role of public health discourse in de-moralising the problem; expanding notions of harm to the child; the construction of the teenage mother as lacking in rational and moral agency; and the construction of her and her child as a social threat. Through an engagement with critiques of teenage pregnancy policy, risk theory and recent developments within the study of ‘parenting culture’, this paper seeks to explain why the ‘teenage mother’ has such symbolic power despite an apparent de-moralisation of sex.
Effect of lapatinib on oral digoxin absorption in patients

The potential for an interaction between lapatinib and absorption of the P‐glycoprotein (ABCB1) substrate digoxin at a therapeutic dose in breast cancer patients was characterized. Seventeen women with HER2‐positive metastatic breast cancer received a single oral 0.5‐mg dose of digoxin on days 1 and 9 and oral lapatinib 1500 mg once daily on days 2 through 9. Digoxin pharmacokinetic parameters were determined on day 1 (digoxin administration alone) and on day 9 (coadministration of lapatinib and digoxin), and parameters were compared to determine the effects of lapatinib on digoxin absorption. Concomitant medications that could affect ABCB1 were accounted for. Lapatinib 1500 mg/day increased digoxin absorption approximately 80%, implicating lapatinib inhibition of intestinal ABCB1‐mediated efflux. In summary, coadministration of lapatinib with narrow therapeutic index drugs that are substrates of ABCB1 should be undertaken with caution and dose adjustment should be considered.
Supporting Proofs for Control-Flow Recovery from Partial Failure Reports

Debugging post-deployment failures is difficult, in part because failure reports from these applications usually provide only partial information about what occurred during the failing execution. We introduce approaches that answer control-flow queries about a failing program’s execution based on failure constraints given as formal languages. A key component of our approach is the introduction of a new class of subregular languages, the unreliable trace languages (UTL), which allow us to answer many common queries in polynomial time. This report supplements the description of these new approaches with formal proofs. Specifically: we prove completeness for our context-insensitive query problem, tightly bind polynomial-time decidability of query recovery to the UTL class, and prove partial correctness for our approach to answering user queries with UTL constraints.
Bilingual LSA-based translation lexicon adaptation for spoken language translation

We present a bilingual LSA (bLSA) framework for translation lexicon adaptation. The idea is to apply marginal adaptation on a translation lexicon so that the lexicon marginals match to indomain marginals. In the framework of speech translation, the bLSA method transfers topic distributions from the source to the target side, such that the translation lexicon can be adapted before translation based on the source document. We evaluated the proposed approach on our Mandarin RT04 spoken language translation system. Results showed that the conditional likelihood on the test sentence pairs is improved significantly using an adapted translation lexicon compared to an unadapted baseline. The proposed approach showed improvement on BLEUscore in SMT. When both the target-side LM and the translation lexicon were adapted and applied simultaneously for SMT decoding, the gain on BLEU-score was more than additive compared to the scenarios when the adapted models were individually applied. Index Terms: Bilingual LSA, Marginal adaptation, Translation lexicon, LM