Miracle-dz/UniFAR-FTUs huggingface dataset:
Next generation mapping reveals novel large genomic rearrangements in prostate cancer

Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.
Motivating Environments: A Systemic Analysis of Four Rural High Schools

Motivating environments include elements across the whole school-as-system, with contributions made by teachers, students, administrators, and factors outside the school in the surrounding community. Positive motivating environments can support self-determination and intrinsic motivation of both students and teachers despite a number of risk factors for school failure. This study addresses schoolwide environments that may promote motivation in areas characterized by isolation and resource limitations. The researcher conducted a systemic analysis of motivationally relevant resources and conditions across four rural schools and communities, using teacher, administrator, school and community profile data. The data indicate that external resources (family, institutional, and community) and internal (motivational) resources are critical elements of the motivating environments in these rural high schools. Teachers' and administrators' motivational perceptions shaped by their prior experiences and current contexts inform the efforts they make to motivate students. Teachers' workplace climate perceptions influence faculty retention and investment. Schools generate unique motivational dynamics through interactions of individual and organizational characteristics.
A low complexity optimization algorithm for zero-forcing precoding under per-antenna power constraints

Zero-forcing beamforming (ZFBF) is a popular pre-coding scheme for MIMO systems. Most of the studies in the literature are under total power constraints. However, the per-antenna power constraints (PAPC) are more realistic. The state-of-the-art method is interior point method which is expensive to realize in practice due to the high computational complexity. Hence, a low complexity zero-forcing precoding scheme under the per-antenna power constraints is proposed in this paper. This is achieved by introducing a regularized dual method. Simulations are carried out to show the effectiveness of the proposed method, which has a low computational complexity. In addition, the algorithm can be implemented in parallel to further reduce the computational complexity.
Petmanship: Understanding Elderly Filipinos' Self-Perceived Health and Self-Esteem Captured from their Lived Experiences with Pet Companions

Understanding of the lived experiences of geriatric clients with pets, particularly in the Western cultures, has been the subject of many studies. However, little is known about how Asian cultures, particularly the Filipino elderly, view their experiences with their pets in regard to their self-esteem and self-perceived health. This phenomenological study purports to capture the essence of the lived experiences of a select group of Filipino elderly with their pet companions in relation to their self-perceived health and self-esteem. A total of five Filipino elderly recruited from the Luzon area were involved in this study and were chosen through the snowballing technique. A three-part instrument was made by the researchers to gather data, namely robotfoto, semistructured interviews, and doodling activities. Field texts were analyzed via structural analysis through the aid of dendogram. Results of both cool and warm analysis have eidetically and interestingly described how the new coinage of petmanship, as introduced in the study, surfaced the functional and the instrumental views of pets relative to the elderly's self-esteem, vis-a-vis their Self-Efficacy Booster and Social Proactivity Builder roles in regard to self-perceived health. The metaphorical images drawn by the Filipino elderly surfaced the Roles Syndrome of Petmanship and the Rules Syndrome of Petmanship.
N-Nitroso compounds and cancer incidence: the European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk Study.

BACKGROUND Humans are exposed to preformed N-nitroso compounds (NOCs) and endogenous NOCs. Several NOCs are potential human carcinogens, including N-nitrosodimethylamine (NDMA), but evidence from population studies is inconsistent. OBJECTIVE We examined the relation between dietary NOCs (NDMA), the endogenous NOC index, and dietary nitrite and cancer incidence in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Norfolk, United Kingdom, study. DESIGN This was a prospective study of 23,363 men and women, aged 40-79 y, who were recruited in 1993-1997 and followed up to 2008. The baseline diet was assessed with food-frequency questionnaires. RESULTS There were 3268 incident cancers after a mean follow-up of 11.4 y. Dietary NDMA intake was significantly associated with increased cancer risk in men and women [hazard ratio (HR): 1.14; 95% CI: 1.03, 1.27; P for trend = 0.03] and in men (HR: 1.24; 95% CI: 1.07, 1.44; P for trend = 0.005) when the highest quartile was compared with the lowest quartile in age- and sex-adjusted analyses but not in multivariate analyses (HR: 1.10; 95% CI: 0.97, 1.24; HR for men: 1.18; 95% CI: 1.00, 1.40; P for trend ≥ 0.05). When continuously analyzed, NDMA was associated with increased risk of gastrointestinal cancers (HR: 1.13; 95% CI: 1.00, 1.28), specifically of rectal cancer (HR: 1.46; 95% CI: 1.16, 1.84) per 1-SD increase after adjustment for age, sex, body mass index, cigarette smoking status, alcohol intake, energy intake, physical activity, education, and menopausal status (in women). The endogenous NOC index and dietary nitrite were not significantly associated with cancer risk. There was a significant interaction between plasma vitamin C concentrations and dietary NDMA intake on cancer incidence (P for interaction < 0.00001). CONCLUSIONS Dietary NOC (NDMA) was associated with a higher gastrointestinal cancer incidence, specifically of rectal cancer. Plasma vitamin C may modify the relation between NDMA exposure and cancer risk.
The Methods and Meanings of Collaborative Team Research

Team research enables the collection of multiple, sometimes conflicting, stories of migration, family, and belonging. Using common qualitative methods within a team research context can stretch these research techniques in productive and instructive ways and proffer new insight and meaning.Therefore, the authors suggest that team research offers an important avenue for both extending qualitative methods and expanding interpretative lenses. To illustrate these points, the authors draw upon their study of the settlement and migration patterns of East African Shia Ismaili Muslims in Vancouver, British Columbia, Canada, and discuss their experiences with focus group effects, the simultaneous household interview strategy, and postinterview dialogues. The article highlights how these three techniques and effects enacted in the team research context helped the authors explicitly locate contradictions, ambiguities, and paradoxes within the narratives of first- and second-generation Ismailis.
Local feature reliability measure using multiview synthetic images for mobile visual search

In this paper, we propose a new database (DB) construction method for the mobile visual search (MVS) system based on the local feature and bag-of-visual-words framework. In MVS, quantization error is unavoidable and causes performance degradation. Typical approaches for visual search extract features from a single view of reference images, though such features are insufficient to manage the quantization error. In this paper, we generate multiview synthetic images and extract local features. These features are resampled according to our novel reliability measure in order to reduce the DB size. Experiments on the three datasets show that the proposed method successfully constructs a robust DB with same size. The proposed method improved the mean average precision compared with a conventional method without changing the searching procedure.
A message propagation model for hybrid vehicular communication protocols

This paper addresses a hybrid approach on message propagation in vehicular networks. Short-range Vehicle-to-Vehicle (V2V) communications cannot always guarantee connectivity to the network cloud, especially when traffic density is very low. By utilizing existing wireless network infrastructure it is possible to greatly enhance the capabilities of short range V2V technologies. Such existing and future communications infrastructure includes UMTS, HSDPA, Wi-Fi, and WiMax. For this multi-network environment we analyze how messages are forwarded by vehicles communicating via a hybrid protocol exploiting both short-range V2V communication schemes and Vehicle-to-Infrastructure (V2I) concepts. The protocol switching from V2V to V2I, and vice versa, occurs through a decision algorithm that considers observed network state. We characterize the bounds of information propagation and compare performance with traditional message propagation based on opportunistic networking. Simulation results show the effectiveness of the proposed hybrid vehicular communication protocol.
Cholecystokinin tetrapeptide induces panic-like attacks in healthy volunteers. Preliminary findings.

• A total of 31 intravenous injections of the tetrapeptide cholecystokinin (30-33) were carried out in ten healthy subjects. In seven subjects, cholecystokinin-4 provoked a short-lasting (one to four minutes) panic-like attack (an intense unexplainable fear) at doses between 20 and 100 μg. In the other three subjects, doses of 80 to 100 μ induced severe anxiety, but no panic-like attack. All subjects experienced severe gastrointestinal symptoms. Pretreatment with lorazepam, but not with meprobamate or naloxone, prevented the psychic effects of cholecystokinin-4 in subjects who had experienced a panic-like attack with the same dose of this peptide. Following the peptide injection, levels of plasma free catecholamines, lactate, and glucose were unchanged, whereas levels of plasma cortisol and prolactin were increased. The intravenous injection of the sulfated cholecystokinin octapeptide (26-33) in two subjects (doses of 35 and 40 μg, respectively) produced severe gastrointestinal symptoms, but failed to induce any anxiety or panic-like attacks. These preliminary findings suggest that cholecystokinin-4 may have a panicinducing effect. It remains to be established if this peptide exerts this effect via a direct activation of central cholecystokinin receptors.
The Role of Positive Life Events on Treatment Outcome during Acute and Maintenance Interpersonal Psychotherapy for Recurrent Major Depressive Disorder

Major Depressive Disorder (MDD) is a highly recurrent and potentially chronic disorder. While much research has focused on the role of severe life events as important risk factors for depression onset, less is known about the relationship between positive life events and MDD. The purpose of the current study was to examine the relationship between positive life events and recovery from an acute episode of depression and maintenance of recovery in the context of Interpersonal Psychotherapy (IPT) treatment in women with recurrent MDD. One hundred thirty-one women who were enrolled in the "Maintenance Psychotherapy in Recurrent Depression" study (MH 49115 E. Frank, PI) entered into maintenance treatment and received at least one Life Events and Difficulties Schedule interview (LEDS; Brown & Harris, 1978). To simultaneously account for both positivity and threat, event ratings were divided into four mutually exclusive categories: provoking, severe, neutral, and positive. A Cox proportional hazards model with each of the four categories of life events included as time-dependent covariates was used to test the cumulative effects of life events on 1) time to remission during the acute treatment phase and 2) time to recurrence during the maintenance phase. Contrary to the hypotheses, there was no relationship between the cumulative experience of positive life events and remission from MDD during the acute treatment phase, nor was there a significant relationship between the cumulative experience of positive life events and episode recurrence. However, the cumulative experience of "neutral" life events was significantly related to episode recurrence, even when controlling for demographic and clinical variables, including personality pathology. This finding suggests that the cumulative effects of seemingly benign "neutral" events may disrupt therapy processes and trigger episode recurrence. Future work is needed to further elucidate the nature of these neutral life events and how they may be related to stress reactivity or stress generation in patients at high risk for MDD recurrence. This may help to clarify the mechanisms by which life events contribute to depression and how best to target these areas in therapy.
End to end evaluation of the ISL View4You broadcast news transcription system

In this paper, we introduce the Interactive Systems Laboratories video indexing and retrieval system 'View4You'. The main components of the system, namely the segmenter, the speech recognizer and the information retrieval engine, are described in detail. In the View4You system, public television newscasts are recorded on a daily basis. The newscasts are automatically segmented and an index is created for each of the segments by means of automatic speech recognition. The user can query the system in natural language. The system returns a list of segments which is sorted by relevance with respect to the user query. By selecting a segment, the user can watch the corresponding part of the news show on his or her computer screen. Several end to end evaluations on real world data, using questions from naive users, are described. By substituting each of the components of the system with a perfect (manually simulated) one, the effect of the components' imperfection on the end to end result can be determined. We show, that the information retrieval component has the largest impact on the system performance, followed by the segmentation. The quality of the speech recognizer, as long as its error rate is below approximately 25%, is shown to have only a relatively small importance.
Drosophila proliferating cell nuclear antigen (cyclin) gene: structure, expression during development, and specific binding of homeodomain proteins to its 5'-flanking region

The genomic and cDNA clones for a Drosophila melanogaster proliferating cell nuclear antigen (PCNA) (cyclin) were isolated and sequenced. The coding sequence for a 260-amino-acid residue polypeptide was interrupted by a single short intron of 60 base pairs (bp), and about 70% of the deduced amino acid sequence of the Drosophila PCNA was identical to the rat and human PCNA polypeptides, with conserved unique repeats of leucine in the C-terminal region. Genomic Southern blot hybridization analysis indicates the presence of a single gene for PCNA per genome. The PCNA mRNA was detected at a high level in adult ovaries, unfertilized eggs, and early embryos and at low levels in the other developmental stages. The major transcription initiation site (cap site) was localized at 89 bp upstream from the ATG codon. Neither a TATA box nor a CAAT box was found within the 600-bp region upstream of the cap site. Clusters of 10 bp of sequence similar to the binding sites for Drosophila proteins containing homeodomains were found in the region from -127 to -413. DNase I footprint analysis revealed that the Drosophila homeodomain proteins coded by even-skipped and zerknüllt genes can specifically bind to these sites. These results suggest that the expression of the PCNA gene is under the control of genes coding for homeodomain proteins.
Boosted acoustic model learning and hypotheses rescoring on the CHiME-3 task

Speech recognition in a realistic noisy environment using multiple microphones is the focal point of the third CHiME challenge. Over the baseline ASR system provided for this challenge, we apply state of the art algorithms for boosting acoustic model learning and hypothesis rescoring to improve the final output. To this aim, we first use the automatic transcription of each channel to re-train the acoustic model for that channel and then we apply linear language model rescoring to find a better solution in the n-best list. LM rescoring is performed using an efficient set of N-gram and Recurrent Neural Network LM (RNNLM) trained on a wisely-selected text set. In the experiments, we show that the proposed approach improves not only the individual channel transcription, but also the enhanced channels produced by MVDR and delay-and-sum beamforming.
( Re ) Enabling support for the CC 2420 chip on the TinyOS Simulator Report for the EE 652 Fall 2011 project at USC

Simulation tools for networked devices are a valuable resource to speed up software development. • TOSSIM (TinyOS SIMulator)[1] is a network simulator that is part of TinyOS [2] (an operating system for networked wireless sensors). • The CC2420 chip [3] is a radio frequency transciever used in many wireless sensor devices. The TOSSIM maintained as part of the main TinyOS trunk does not implement simulation of the CC2420 chip. This has been succesfully implemented outside the primary TinyOS trunk in the past [4], however this support has not been maintained with newer versions of TinyOS. In this paper we describe in detail the process that was followed to add CC2420 simulation support to the latest TOSSIM. We also describe our evaluation method to confirm that the implementation is functional and accurate. We publish the results of our evaluations and show that the CC2420 is succesfully simulated within the TOSSIM environment.
Causality in Scale Space as an Approach to Change Detection

Kernel density estimation and kernel regression are useful ways to visualize and assess the structure of data. Using these techniques we define a temporal scale space as the vector space spanned by bandwidth and a temporal variable. In this space significance regions that reflect a significant derivative in the kernel smooth similar to those of SiZer (Significant Zero-crossings of derivatives) are indicated. Significance regions are established by hypothesis tests for significant gradient at every point in scale space. Causality is imposed onto the space by restricting to kernels with left-bounded or finite support and shifting kernels forward. We show that these adjustments to the methodology enable early detection of changes in time series constituting live surveillance systems of either count data or unevenly sampled measurements. Warning delays are comparable to standard techniques though comparison shows that other techniques may be better suited for single-scale problems. Our method reliably detects change points even with little to no knowledge about the relevant scale of the problem. Hence the technique will be applicable for a large variety of sources without tailoring. Furthermore this technique enables us to obtain a retrospective reliable interval estimate of the time of a change point rather than a point estimate. We apply the technique to disease outbreak detection based on laboratory confirmed cases for pertussis and influenza as well as blood glucose concentration obtained from patients with diabetes type 1.
Electronic-database Information

Arnason E (2003) Genetic heterogeneity of Icelanders. Ann Hum Genet 67:5–16 Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V (2002) The fingerprint of phantom mutations in mitochondrial DNA data. Am J Hum Genet 71:1150–1160 Dennis C (2003) Error reports threaten to unravel databases of mitochondrial DNA. Nature 421:773–774 Forster P (2003) To err is human. Ann Hum Genet 67:2–4 Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, Ghosh SS, Olefsky JM, Beal MF, Davis RE, Howell N (2002) Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet 70:1152–1170 (erratum 71:448–449) Vernesi C. Fuselli S, Castri L, Bertorelle G, Barbujani G (2002) Mitochondrial diversity in linguistic isolates of the Alps: a reappraisal. Hum Biol 74:725–730
Clinically relevant morphological structures in breast cancer represent transcriptionally distinct tumor cell populations with varied degrees of epithelial-mesenchymal transition and CD44+CD24- stemness

Intratumor morphological heterogeneity in breast cancer is represented by different morphological structures (tubular, alveolar, solid, trabecular, and discrete) and contributes to poor prognosis; however, the mechanisms involved remain unclear. In this study, we performed 3D imaging, laser microdissection-assisted array comparative genomic hybridization and gene expression microarray analysis of different morphological structures and examined their association with the standard immunohistochemistry scorings and CD44+CD24- cancer stem cells. We found that the intratumor morphological heterogeneity is not associated with chromosomal aberrations. By contrast, morphological structures were characterized by specific gene expression profiles and signaling pathways and significantly differed in progesterone receptor and Ki-67 expression. Most importantly, we observed significant differences between structures in the number of expressed genes of the epithelial and mesenchymal phenotypes and the association with cancer invasion pathways. Tubular (tube-shaped) and alveolar (spheroid-shaped) structures were transcriptionally similar and demonstrated co-expression of epithelial and mesenchymal markers. Solid (large shapeless) structures retained epithelial features but demonstrated an increase in mesenchymal traits and collective cell migration hallmarks. Mesenchymal genes and cancer invasion pathways, as well as Ki-67 expression, were enriched in trabecular (one/two rows of tumor cells) and discrete groups (single cells and/or arrangements of 2-5 cells). Surprisingly, the number of CD44+CD24- cells was found to be the lowest in discrete groups and the highest in alveolar and solid structures. Overall, our findings indicate the association of intratumor morphological heterogeneity in breast cancer with the epithelial-mesenchymal transition and CD44+CD24- stemness and the appeal of this heterogeneity as a model for the study of cancer invasion.