LLukas22/scidocs huggingface dataset:
Discriminative modelling of context-specific amino acid substitution probabilities

MOTIVATION
Protein sequence searching and alignment are fundamental tools of modern biology. Alignments are assessed using their similarity scores, essentially the sum of substitution matrix scores over all pairs of aligned amino acids. We previously proposed a generative probabilistic method that yields scores that take the sequence context around each aligned residue into account. This method showed drastically improved sensitivity and alignment quality compared with standard substitution matrix-based alignment.


RESULTS
Here, we develop an alternative discriminative approach to predict sequence context-specific substitution scores. We applied our approach to compute context-specific sequence profiles for Basic Local Alignment Search Tool (BLAST) and compared the new tool (CS-BLASTdis) to BLAST and the previous context-specific version (CS-BLASTgen). On a dataset filtered to 20% maximum sequence identity, CS-BLASTdisis was 51% more sensitive than BLAST and 17% more sensitive than CS-BLASTgenin, detecting remote homologues at 10% false discovery rate. At 30% maximum sequence identity, its alignments contain 21 and 12% more correct residue pairs than those of BLAST and CS-BLASTgen, respectively. Clear improvements are also seen when the approach is combined with PSI-BLAST and HHblits. We believe the context-specific approach should replace substitution matrices wherever sensitivity and alignment quality are critical.
Strategies to improve repeat fecal occult blood testing cancer screening.

BACKGROUND
A comparative effectiveness intervention by this team improved initial fecal occult blood testing (FOBT) rates from 3% to 53% among community clinic patients. The purpose of this study was to evaluate the effectiveness and costs associated with a literacy-informed intervention on repeat FOBT testing.


METHODS
Between 2008 and 2011, a three-arm quasi-experiential comparative effectiveness evaluation was conducted in eight community clinics in Louisiana. Clinics were randomly assigned to receive: enhanced care, a screening recommendation, and FOBT kit annually; a brief educational intervention where patients additionally received a literacy appropriate pamphlet and simplified FOBT instructions; or nurse support where a nurse manager provided the education and followed up with phone support. In year 2, all materials were mailed. The study consisted of 461 patients, ages 50 to 85 years, with a negative initial FOBT.


RESULTS
Repeat FOBT rates were 38% enhanced care, 33% education, and 59% with nurse support (P = 0.017). After adjusting for age, race, gender, and literacy, patients receiving nurse support were 1.46 times more likely to complete repeat FOBT screening than those receiving education [95% confidence interval (CI), 1.14-1.06; P = 0.002] and 1.45 times more likely than those in enhanced care but this was not significant (95% CI, 0.93-2.26; P = 0.10). The incremental cost per additional person screened was $2,450 for nurse over enhanced care.


CONCLUSION
A mailed pamphlet and FOBT with simplified instructions did not improve annual screening.


IMPACT
Telephone outreach by a nurse manager was effective in improving rates of repeat FOBT, yet this may be too costly for community clinics.
Extraoperative functional mapping of motor areas in epileptic patients by high-frequency cortical stimulation.

OBJECT
The aim of this study was to investigate the usefulness of a short train of high-frequency (500 Hz) cortical stimulation to delineate the primary motor cortex (MI), supplementary motor area (SMA), primary somatosensory cortex (SI), supplementary sensory area (SSA), negative motor area (NMA), and supplementary negative motor area (SNMA) in patients with epilepsy who were undergoing functional mapping.


METHODS
Seventeen patients were studied, all of whom underwent functional mapping using 50-Hz electrical stimulation. After these clinical evaluations, cortical stimulations with a short train of electrical pulses at 500 Hz were performed through subdural electrodes placed at the MI, SMA, SI, SSA, NMA, and SNMA, which had been identified by 50-Hz stimulation, and surrounding cortical areas, while surface electromyography readings were recorded.


RESULTS
Stimulation of the MI elicited motor evoked potentials (MEPs) in contralateral muscles. Stimulation of the SMA also induced MEPs in contralateral muscles but with longer latencies compared with the MI stimulation. Stimulation of the SMA did not elicit MEPs in ipsilateral muscles. Stimulation of the SI, SSA, NMA, and SNMA did not induce MEPs in any muscle. In one patient, MEPs were elicited without seizure induction by 500-Hz stimulation of the electrodes, whereas a 50-Hz stimulation of the same electrodes induced his habitual seizures.


CONCLUSIONS
Extraoperative high-frequency stimulation with MEP monitoring is a useful complementary method for cortical mapping without inducing seizure. Stimulation of SMA induces MEPs in contralateral muscles, with longer latencies compared with the stimulation of MI. This finding may be useful for the differentiation between MI and SMA, especially in the foot motor areas.
Early psychological reactions in parents of children with a life threatening illness within a pediatric hospital setting.

RESEARCH IN CONTEXT
Parents of children with life threatening illness or injuries are at elevated risk of distress reactions, involving symptoms of acute stress disorder, depression and anxiety. Currently, the impact of child illness factors is unclear, and to date research systematically examining the prevalence of these psychological reactions across different illness groups with an acute life threat is sparse. This is important to explore given that studies show that parent functioning impacts on the psychological adjustment and recovery of the ill child. WHAT DOES THIS STUDY ADD?: At four weeks following a child's diagnosis of a serious illness, 49-54% of parents met DSM-IV criteria for acute stress disorder, across a number of illness groups, whereas 15-27% of parents were in the moderate/severe range for depression and anxiety, and 25-31% for stress. Results from this study demonstrate that rates and severity of these psychological reactions in parents of seriously ill children do not vary according to illness type.


BACKGROUND
A life threatening childhood illness/injury can lead to significant distress reactions in parents, with independent studies finding such reactions in several different illness groups. To date, there is limited research systematically comparing the prevalence of adverse parental psychological reactions across different childhood illness groups with an acute life threat. This study aimed to investigate the frequency and severity of symptoms of acute traumatic stress, depression, anxiety and general stress in parents, following admission of their child to hospital for a life threatening illness. The study also aimed to explore the relationship between these symptoms, and to determine whether they differ according to illness/injury.


METHODS
Cross-sectional data from a prospective, longitudinal study are reported. Participants were 194 parents of 145 children (49 couples), admitted to cardiology (n=53), oncology (n=40) and pediatric intensive care units (n=52), for serious illnesses/injuries. Parents completed self-report questionnaires within four weeks of hospital admission.


RESULTS
Rates of acute traumatic stress (P=0.262), depression (P=0.525), anxiety (P=0.453) and general stress symptoms (P=0.720) in parents were comparable across illness type, with 49-54% reaching criteria for acute stress disorder, 15-27% having clinical levels of depression and anxiety, and 25-31% for general stress. Anxiety was most strongly associated with acute traumatic stress (r=0.56), closely followed by stress (r=0.52) and depression (r=0.49), with all correlations highly significant (P<0.001).


CONCLUSIONS
These findings provide evidence that the child's medical condition is not associated with parents' experience of clinically significant psychological symptoms, and emphasize the importance for health care providers to be aware of these potential psychological reactions in parents, regardless of the type of illness.
A Hybrid Adaptive Unscented Kalman Filter Algorithm

In order to overcome the limitation of the traditional adaptive Unscented Kalman Filtering (UKF) algorithm in noise covariance estimation for statement and measurement, we propose a hybrid adaptive UKF algorithm based on combining Maximum a posteriori (MAP) criterion and Maximum likelihood (ML) criterion, in this paper. First, to prevent the actual noise covariance deviating from the true value which can lead to the state estimation error and arouse the filtering divergence, a real-time covariance matrices estimation algorithm based on hybrid MAP and ML is proposed for obtaining the statement and measurement noises covariance, respectively; and then, a balance equation the two kinds of covariance matrix is structured in this proposed to minimize the statement estimation error. Compared with the UFK based MAP and based ML, the proposed algorithm provides better convergence and stability.
Intergenerational solidarity and the structure of adult child-parent relationships in American families

The authors investigate the structure of intergenerational cohesion by examining social-psychological, structural, and transactional aspects of adult child–parent relations. The authors use latent class analysis to develop a typology based on three underlying dimensions of intergenerational solidarity: affinity, opportunity structure, and function. The same five types are found for relations with both mothers and fathers: tight-knit, sociable, intimate but distant, obligatory, and detached. Relationship types are also differentiated by sociodemographic characteristics; relations with fathers and divorced parents tended to have the weakest cohesion. The authors conclude that adult intergenerational relationships in American families are structurally diverse but generally possess the potential to serve their members’ needs.
Anhedonia in schizophrenia and major depression: state or trait?

BACKGROUND
In schizophrenia and major depressive disorder, anhedonia (a loss of capacity to feel pleasure) had differently been considered as a premorbid personological trait or as a main symptom of their clinical picture. The aims of this study were to examine the pathological features of anhedonia in schizophrenic and depressed patients, and to investigate its clinical relations with general psychopathology (negative, positive, and depressive dimensions).


METHODS
A total of 145 patients (80 schizophrenics and 65 depressed subjects) were assessed using the Physical Anhedonia Scale and the Social Anhedonia Scale (PAS and SAS, respectively), the Scales for the Assessment of Positive and Negative Symptoms (SAPS and SANS, respectively), the Calgary Depression Scale for Schizophrenics (CDSS), and the Hamilton Depression Rating Scale (HDRS). The statistical analysis was performed in two steps. First, the schizophrenic and depressed samples were dichotomised into 'anhedonic' and 'normal hedonic' subgroups (according to the 'double (PAS/SAS) cut-off') and were compared on the general psychopathology scores using the Mann-Whitney Z test. Subsequently, for the total schizophrenic and depressed samples, Spearman correlations were calculated to examine the relation between anhedonia ratings and the other psychopathological parameters.


RESULTS
In the schizophrenic sample, anhedonia reached high significant levels only in 45% of patients (n = 36). This 'anhedonic' subgroup was distinguished by high scores in the disorganisation and negative dimensions. Positive correlations of anhedonia with disorganised and negative symptoms were also been detected. In the depressed sample, anhedonia reached high significant levels in only 36.9% of subjects (n = 24). This 'anhedonic' subgroup as distinguished by high scores in the depression severity and negative dimensions. Positive correlations of anhedonia with depressive and negative symptoms were also been detected.


CONCLUSION
In the schizophrenic sample, anhedonia seems to be a specific subjective psychopathological experience of the negative and disorganised forms of schizophrenia. In the depressed sample, anhedonia seems to be a specific subjective psychopathological experience of those major depressive disorder forms with a marked clinical depression severity.
Interactive wormhole detection and evaluation

Received: 23 June 2006 Revised: 31 July 2006 Accepted: 21 October 2006 Online publication date: 25 January 2007 Abstract Wormhole attacks in wireless networks can severely deteriorate network performance and compromise security through spoiling the routing protocols and weakening the security enhancements. This paper develops an approach, interactive visualization of wormholes (IVoW), to monitor and detect such attacks in large-scale wireless networks in real time. We characterize the topology features of a network under wormhole attacks through the node position changes and visualize the information at dynamically adjusted scales. We integrate an automatic detection algorithm with appropriate user interactions to handle complicated scenarios that include a large number of moving nodes and multiple wormhole attackers. Various visual forms have been adopted to assist in the understanding and analysis of reconstructed network topology and to improve the detection accuracy. Extended simulation has demonstrated that the proposed approach can effectively locate the fake neighbor connections without introducing many false alarms. IVoW does not require the wireless nodes to be equipped with any special hardware, thus avoiding any additional cost. We have performed user studies to evaluate the effectiveness of our approach and demonstrate that visual analysis can be successfully combined with network security mechanisms to greatly improve intrusion detection capabilities. Information Visualization (2007) 6, 3--17. doi:10.1057/palgrave.ivs.9500144
Recent skin injuries in children with motor disabilities.

OBJECTIVE
To determine the frequency of recent skin injuries in children with neuromotor disabilities and its association with disability.


DESIGN
Cross-sectional study of 168 children with neuromotor disabilities aged 2-16 years.


SETTING
Two outpatient child rehabilitation centres.


MAIN OUTCOME MEASURES
Children were classified as unrestricted walkers, restricted walkers or wheelchair dependent. Each participant's body surface was systematically examined for recent skin injuries with the exception of the anal-genital area.


RESULTS
The mean age of our sample was 7.8 (SD 3.7) years with a 3:2 male/female ratio. Overall, 64% had cerebral palsy, 17% a neuromuscular disease and 19% other motor disabilities. Participants had on average 5.3 (SD 4.5) recent skin injuries (max 19), of which 2.5 were bruises (SD 3.3, max 16), 2.4 were abrasions, scratches or cuts (SD 3.0, max 16) and 0.4 were pressure lesions (SD 0.8, max 4). There was a significant decrease in the frequency of recent skin injuries and of bruises with increasing severity of motor disability. Most of this variation was accounted for by injuries to the lower limbs. There were no significant effects of gender, learning disabilities or other comorbidities.


CONCLUSIONS
Children with neuromotor disabilities present a progressive reduction in the number of skin injuries with decreasing mobility. Therefore, recent skin injuries in this population which are unusual by their number, appearance or distribution, should raise at least the same level of suspicion for physical abuse as in children without disabilities.
A phase II randomized study comparing navelbine and capecitabine (Navcap) followed either by Navcap or by weekly docetaxel in the first-line treatment of HER-2/neu negative metastatic breast cancer.

UNLABELLED
Following the proven efficacy and tolerability of Navcap and Navcap followed by docetaxel in the treatment of MBC, a phase II randomized study was initiated to assess the ORR of both arms in the first-line setting of MBC. Patients with no prior chemotherapy for MBC and HER-2/neu negative were eligible. All patients received Navcap (V 25 mg/m2 on d1 and d8 and C 825 mg/m2 bid D1-14 q3w) for a total of 4 cycles. Patients progressing under Navcap were withdrawn and received docetaxel as second-line treatment. Patients responding or stable were randomized to 2 arms: 4 cycles of Navcap (A) or 12 weekly docetaxel (25 mg/m²/week) (B). From July 2004 to July 2008, a total of 106 patients were enrolled. Ninety-four patients were evaluable before randomization, with a clinical benefit of 58%. Twenty-one patients (22%) had disease progression and were therefore not randomized. Forty-one patients were randomized to arm A and 29 patients to arm B. ORRs were 56 and 71% in arms A and B, respectively. The median time to progression and overall survival were 10 and 35 months in arm A and 12 and 37 months in arm B. Adverse events were mild. Arm A: grade 3-4 neutropenia (10%), grade 3 anemia (5%). Arm B: grade 3 neutropenia (6%), grade 3 anemia (6.2%), and grade 2 alopecia (12%).


CONCLUSION
Both Navcap and Navcap followed by Docetaxel regimens were tolerated with manageable toxicity, offering consistent activities in terms of response rate for metastatic breast cancer patients.
NoC Emulation on FPGA: HW/SW Synergy for NoC Features Exploration

Current Systems-On-Chip (SoC) execute applications that demand extensive parallel processing. Networks-On-Chip (NoC) provide a structured way of realizing interconnections on silicon, and obviate the limitations of bus-based solution. NoCs can have regular or ad hoc topologies, and functional validation is essential to assess their correctness and performance. In this paper, we present a flexible emulation environment implemented on an FPGA that is suitable to explore, evaluate and compare a wide range of NoC solutions with a very limited effort. We also present an automated way to perform NoC features exploration using the interaction HW/SW on an FPGA. Our experimental results show a speed-up of four orders of magnitude with respect to cycleaccurate HDL simulation, while retaining cycle accuracy. With our emulation framework, designers can explore and optimize a various range of solutions, as well as characterize quickly performance figures.
Robust Optimization of Large-Scale Systems

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Effect of tiotropium bromide on the cardiovascular response to exercise in COPD.

INTRODUCTION
Exercise limitation and exertional dyspnea are important symptoms of chronic obstructive pulmonary disease (COPD), which may be partially relieved by tiotropium. Although the mechanism of relief is multifactorial, improved dynamic ventilatory mechanics appear to be important. It is not however known whether tiotropium may also act by improving cardiovascular function during exercise.


METHODS
We conducted a randomized, placebo-controlled crossover study in 18 COPD subjects with a FEV(1) 40+/-3% predicted (mean+/-SEM). Subjects inhaled either tiotropium 18 microg or placebo once daily for 7-10 days then the other intervention for a further 7-10 days after a 35-day washout period. Subjects performed constant work rate cycle exercise at 75% of maximum after each treatment period. Heart rate, blood pressure, oxygen uptake, operating lung volumes and breathing pattern were measured.


RESULTS
Heart rate was 7 beats/min lower at rest and throughout exercise with tiotropium compared to placebo (p=0.001). Oxygen uptake was unchanged throughout exercise. Oxygen pulse on exercise was greater by 7.4% (p<0.01) and systolic blood pressure was lower by 7 mmHg (p=0.03). The cardiac rate pressure product was reduced by 7.6% (p<0.01) with tiotropium. Exercise endurance tended to be greater with tiotropium. Reduction in heart rate on exercise correlated with an increase in inspiratory reserve volume (r=-0.50, p=0.04).


CONCLUSION
Tiotropium may improve cardiac as well as pulmonary function during exercise in COPD. We suggest that this effect may be due, in part, to improved cardiopulmonary interaction as a result of mechanical unloading of the ventilatory muscles however further study is required.
A Novel Role-Based Movie Scene Segmentation Method

Semantic scene segmentation is a crucial step in movie video analysis and extensive research efforts have been devoted to this area. However, previous methods are heavily relying on video content itself, which are lack of objective evaluation criterion and necessary semantic link due to the semantic gap. In this paper, we propose a novel role-based approach for movie scene segmentation using script. Script is a text description of movie content that contains the scene structure information and related character names, which can be regarded as an objective evaluation criterion and useful external reference. The main novelty of our approach is that we convert the movie scene segmentation into a movie-script alignment problem and propose a HMM alignment algorithm to map the script scene structure to the movie content. The promising results obtained from three Hollywood movies demonstrate the effectiveness of our proposed approach.
Regional differences in white matter breakdown between frontotemporal dementia and early-onset Alzheimer's disease.

BACKGROUND
White matter abnormalities have been associated with both behavioral variant frontotemporal dementia (bvFTD) and Alzheimer's disease (AD).


OBJECTIVE
Using MRI diffusion tensor imaging (DTI) measures, we compared white matter integrity between patients with bvFTD and those with early-onset AD and correlated these biomarkers with behavioral symptoms involving emotional blunting.


METHODS
We studied 8 bvFTD and 12 AD patients as well as 12 demographically-matched healthy controls (NCs). Using four DTI metrics (fractional anisotropy, axial diffusivity, radial diffusivity, and mean diffusivity), we assessed the frontal lobes (FWM) and genu of the corpus callosum (GWM), which are vulnerable late-myelinating regions, and a contrasting early-myelinating region (splenium of the corpus callosum). The Scale for Emotional Blunting Scale (SEB) was used to assess emotional functioning of the study participants.


RESULTS
Compared to AD patients and NCs, the bvFTD subjects exhibited significantly worse FWM and GWM integrity on all four DTI metrics sensitive to myelin and axonal integrity. In contrast, AD patients showed a numerical trend toward worse splenium of the corpus callosum integrity than bvFTD and NC groups. Significant associations between SEB ratings and GWM DTI measures were demonstrated in the combined bvFTD and AD sample. When examined separately, these relationships remained robust for the bvFTD group but not the AD group.


CONCLUSIONS
The regional DTI alterations suggest that FTD and AD are each associated with a characteristic distribution of white matter degradation. White matter breakdown in late-myelinating regions was associated with symptoms of emotional blunting, particularly within the bvFTD group.