Miracle-dz/UniFAR-FTUs huggingface dataset:
Indexing Highly Repetitive String Collections, Part II

Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through applications like bioinformatics, the string collections experienced a growth that outperforms Moore’s Law and challenges our ability of handling them even in compressed form. It turns out, fortunately, that many of these rapidly growing string collections are highly repetitive, so that their information content is orders of magnitude lower than their plain size. The statistical compression methods used for classical collections, however, are blind to this repetitiveness, and therefore a new set of techniques has been developed to properly exploit it. The resulting indexes form a new generation of data structures able to handle the huge repetitive string collections that we are facing. In this survey, formed by two parts, we cover the algorithmic developments that have led to these data structures. In this second part, we describe the fundamental algorithmic ideas and data structures that form the base of all the existing indexes, and the various concrete structures that have been proposed, comparing them both in theoretical and practical aspects, and uncovering some new combinations. We conclude with the current challenges in this fascinating field.
Phylogenetical analysis of partially sequenced cytb gene of Haemoproteus columbae in pigeons and its pathological lesions in Egypt.

Background Haemoproteus columbae is widely distributed in tropical and subtropical regions, causing pseudomalaria in pigeons. Aims The current study aimed to characterize the phylogenetic position of H. columbae in pigeons in Sharkia province, Egypt, based on partial sequencing of the cytb gene as the conserved regions. The "DNA barcode" of the cytb gene helps in designing primers that can be used to amplify the same gene in the related haemosporidians. Methods: One hundered blood samples were collected from domestic pigeons to identify H. columbae by polymerase chain reaction (PCR) and detect its relationship with other related haemosporidians. Results Weight losses of 60%, anemia 40%, low growth rates 26.67%, diarrhea 76.67%, dyspnea 66.67%, some neurological symptoms 33.33%, and death 16.67% were observed in the studied birds. Post-mortem examinations showed chocolate-brown appearance of the livers of the birds and congested parenchymatous organs. Microscopical examinations of Giemsa stained blood smears (n=100) revealed a 30% infection rate. The obtained infection percentages were more pronounced in males (35.71%) than females (16.66%) and more in adults (57.14%) than young pigeons (15.38%). The present sequence of H. columbae was deposited in GenBank under accession No.: MH345964 and shows 100% identity with other related Haemoproteus species in the Sao Paulo Zoo, Brazil (KU131585 and KU131583) and the UK (KX832581 and KX832586). Conclusion This study concluded that the accurate diagnosis of H. coulmbae infection in pigeons by specific primers will help with the early treatment of affected cases, especially in the presence of the immature forms, and can thus avoid the noticed clinical signs and the induced pathological lesions mentioned in our study.
Event- and time-based prospective memory in hemodialysis patients

Abstract Objective The present study investigated whether hemodialysis (HD) patients exhibit future memory impairment (PM; the capability of remembering to perform expected future actions) and exploring relevant factors of PM task performance. Methods Sixty HD patients and 60 healthy controls matched by age are enrolled in the Mini-Mental State Examination (MMSE), Finger Span Test (DST), Oral Fluency Test (VFT), Ray Auditory Oral Learning Test (RAVLT), Received Stroop Color Word Interference Test (SCWT), and event-based PM (EBPM) and time-based PM (TBPM). Results There were no significant difference between the patients and controls in the DST-Forward digit span (9.00 ± 1.25 versus 8.97 ± 1.33, p = 0.96), the DST-Backward digit span (5.23 ± 1.98 versus. 4.60 ± 1.65, p = 0.11), the RAVLT of delayed recall (7.28 ± 2.36 versus 6.87 ± 3.33, p = 0.09) and the VFT for animals (16.70 ± 3.50 versus 17.68 ± 5.45, p = 0.56). By comparison, patients had a much worse performance than controls on the MMSE (29.10 ± 0.84 versus 28.33 ± 0.77, p < 0.001), the RAVLT of total recall (44.47 ± 5.82 versus 40.03 ± 10.46, p < 0.001) and delayed recognition (6.93 ± 1.49 versus 5.4 ± 1.33, p < 0.001), the SCWT reaction time in reading (6.47 ± 1.05 versus 7.47 ± 1.86, p < 0.001), color naming (9.07 ± 1.29 versus 11.43 ± 2.34, p < 0.001), interference (8.78 ± 1.92 versus 10.22 ± 2.91, p < 0.001) and inhibition/switching (14.53 ± 2.90 versus 19.85 ± 4.69, p < 0.001), the VFT for fruit (17.47 ± 3.18 versus 15.92 ± 4.56, p < 0.001), the EBPM task (7.85 ± 0.40 versus 7.08 ± 1.43, p = 0.01), and the TBPM task (3.30 ± 1.31 versus 2.26 ± 1.82, p < 0.001). Conclusions Our results suggest that EBPM and TBPM are impaired in HD patients and that PM may be applied to help evaluate cognitive dysfunction in HD patients.
Genetic Information and Precision Medicine in Hearing Loss

Copyright © 2020 by Korean Society of Otorhinolaryngology-Head and Neck Surgery. This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Clinical and Experimental Otorhinolaryngology Vol. 13, No. 4: 315-317, November 2020 https://doi.org/10.21053/ceo.2020. 01606
Cohort profile: The Forzani & MacPhail Colon Cancer Screening Centre biorepository, Calgary, Alberta

Purpose The Colon Cancer Screening Centre (CCSC) biorepository (Calgary, Canada) supports a wide range of research topics related to colorectal cancer (CRC) by collecting, and storing biospecimens (blood, urine, normal colon tissue) from consenting patient participants. Housing unique biospecimens along with detailed participant lifestyle and health history questionnaire data, the CCSC biorepository can support a variety of research related to CRC risk factors, biomarkers, genetic causes and more. Participants Currently, 2292 average risk CRC patients have consented to participate in the CCSC cohort and have provided stored biospecimens. The collected samples and data provide important high-quality materials for research, discovery and evaluation related to CRC screening and carcinogenesis and is available for access by outside researchers. In addition to biological samples, the CCSC collects detailed patient information on their lifestyle, physical activity and dietary patterns through questionnaires at the time of their enrolment. Findings to date The majority of participants (75%) are between 50 and 64 years of age. Women make up 46% (1055) of the cohort. Additional characteristics of the cohort included 44% reporting a body mass index of 25–30 kg/m2 (overweight), 53% having never smoked tobacco and 13% having a family member with CRC. Future plans The CCSC cohort plans to include the recruitment of high risk CRC cohorts. High-risk participants would comprise patients with a positive faecal immunochemical test and family history of CRC.
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues

Abstract Splicing is an essential step of RNA processing for multi-exon genes, in which introns are removed from a precursor RNA, thereby producing mature RNAs containing splice junctions. Here, we develope the RJunBase (www.RJunBase.org), a web-accessible database of three types of RNA splice junctions (linear, back-splice, and fusion junctions) that are derived from RNA-seq data of non-cancerous and cancerous tissues. The RJunBase aims to integrate and characterize all RNA splice junctions of both healthy or pathological human cells and tissues. This new database facilitates the visualization of the gene-level splicing pattern and the junction-level expression profile, as well as the demonstration of unannotated and tumor-specific junctions. The first release of RJunBase contains 682 017 linear junctions, 225 949 back-splice junctions and 34 733 fusion junctions across 18 084 non-cancerous and 11 540 cancerous samples. RJunBase can aid researchers in discovering new splicing-associated targets and provide insights into the identification and assessment of potential neoepitopes for cancer treatment.
Lower abdominal and pelvic radiation and testicular germ cell tumor risk

Background Testicular germ cell tumor (TGCT) incidence has increased in recent decades along with the use and dose of diagnostic radiation. Here we examine the association between reported exposure to diagnostic radiation and TGCT risk. Methods We conducted a case-control study of men with and without TGCT recruited from hospital- and population-based settings. Participants reported on exposures to 1) x-ray or CT below the waist and 2) lower GI series or barium enema, which consists of a series of x-rays of the colon. We also derived a combined measure of exposure. We used logistic regression to determine the risk of developing TGCT according to categories of exposures (0, 1–2, or ≥3 exposures) and age at first exposure, adjusting for age, year of birth, race, county, body mass index at diagnosis, family history of TGCT, and personal history of cryptorchidism. Results There were 315 men with TGCT and 931 men without TGCT in our study. Compared to no exposures, risk of TGCT was significantly elevated among those reporting at least three exposures to x-ray or CT (OR≥3 exposures, 1.78; 95% CI, 1.15–2.76; p = 0.010), lower GI series or barium enema (OR≥3 exposures, 4.58; 95% CI, 2.39–8.76; p<0.001), and the combined exposure variable (OR≥3 exposures, 1.59; 95% CI, 1.05–2.42; p = 0.029). The risk of TGCT was elevated for those exposed to diagnostic radiation at age 0–10 years, compared to those first exposed at age 18 years or later, although this association did not reach statistical significance (OR, 2.00; 95% CI, 0.91–4.42; p = 0.086). Conclusions Exposure to diagnostic radiation below the waist may increase TGCT risk. If these results are validated, efforts to reduce diagnostic radiation doses to the testes should be prioritized.
Genetic Structure of Sympatric Populations of Female Lutzomyia Longipalpis (Diptera: Psychodidae) In Sobral and Caririaçu, Ceará State, Brazil

Objectives: Accurate identification of these insects is critical to avoiding mistakes in the recognition of vector and non-vector species, so the invariant phenotypic patterns displayed by the females of L. longipalpis require the implementation of molecular methods of identification. Our goal was to examine genetic variation in the females of L. longipalpis using the SNPs reported in the males of this vector species. Methods: We trapped sand flies near houses and domestic animal shelters at two localities in the state of Ceara, Brazil, using two to five CDC miniature light traps. Genomic DNA was separately extracted from each female using 100 μl of Chelex resin, and a 525 bp fragment of the period gene was used to assess genetic polymorphism in the two geographically isolated populations. Results: The results indicate the presence of three fixed polymorphisms (T124C, C171T, and C424T) within this gene. Genetic structure analysis indicated that the studied L. longipalpis populations can be divided into two main subgroups (1S-like and 2S-like), with the ad hoc quantity supporting the number K = 2. Conclusion: Collectively, our results suggest a direct relationship between the number of spots found in the males’ tergites and the genetic variation observed in the L. longipalpis females in the state of Ceara. The SNPs observed in the period gene will be useful for future studies of molecular eco-epidemiology in areas where these species occur in sympatry.
Differentiation of Self and Mate Retention Behaviors: The Mediating Role of Communication Patterns

Differentiation of self refers to the capacity of individuals to manage their emotions, remain thoughtful in strong emotional experiences, and the ability to experience intimacy and independence in relationships. Individual differences in differentiation of self may influence the performance of mate retention behaviors. Because poorly differentiated individuals find separation and rejection unbearable and anxiety-provoking, we hypothesized that different levels of differentiation is related to different strategies of mate retention behaviors. However, little empirical attention has been given to the relationship between differentiation of self and mate retention behaviors, particularly in non-individualistic cultures. We aimed to investigate the mediating role of communication patterns in the relationship between differentiation of self and mate retention behaviors. The sample included 282 married individuals from Community Centers (some neighborhoods in Tehran, Iran). The results supported the associations between mate retention behaviors and differentiation of self, and also showed that communication patterns mediate this relationship. This study improves our understanding of differentiation of self and mate retention behaviors in the context of long-term committed relationships from an evolutionary psychological perspective.
Influence of the Genetic Background on Allergic Rhinitis Models in Mice

Copyright © 2020 by Korean Society of Otorhinolaryngology-Head and Neck Surgery. This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Clinical and Experimental Otorhinolaryngology Vol. 13, No. 4: 322-323, November 2020 https://doi.org/10.21053/ceo.2020. 00892
Impact of Laboratory Methods and Gene Targets on Detection of Streptococcus pneumoniae in Isolates and Clinical Specimens.

Background Timely identification of Streptococcus pneumoniae infections can lead to a decrease in mortality rates. Differentiation of S. pneumoniae from other similar species using traditional culture-based and molecular methods is problematic. In this study, we assessed the efficacy of identifying the blpA and lytA for the detection of S. pneumoniae from isolates and various clinical samples using molecular methods. Methods A total of 440 clinical samples were collected from patients with suspected invasive pneumococcal infections during February 2016 to October 2018. Biochemical tests were used to confirm the dubious colonies on 5% sheep blood agar. Fifty-seven confirmed isolates, 57 culture-positive samples, and 57 culture-negative samples were analyzed for the presence of blpA and lytA using both conventional and real-time PCR. Results All the isolates and culture-positive samples were positive for blpA and lytA by both PCR methods. Of the 57 culture-negative samples, conventional and real-time PCR amplified blpA from six and two samples, and lytA from seven and two samples, respectively. Conclusion The specificity of real-time PCR assay was significantly higher than that of conventional PCR for the identification of S. pneumoniae. In addition, it is suggested that respiratory secretions are not suitable specimen for direct diagnosis of pneumococcal infections.
Oscillations in the central brain of Drosophila are phase locked to attended visual features

Significance There is increasing evidence that even the smallest animal brains provide a capacity for selective attention and subjective awareness, but it is unknown if similar mechanisms might be employed as in higher animals. Recent work in insects highlights a brain structure, the central complex (CX), which could support selective attention processes. Recording from the CX of behaving flies making decisions in a virtual reality environment, we show that visual selection is achieved by phase-controlled endogenous 20- to 30-Hz oscillations that lock onto temporal features of attended visual objects. This suggests an oscillation-driven binding mechanism in the insect brain that employs a similar beta frequency range as has been observed for feature binding in humans. Object-based attention describes the brain’s capacity to prioritize one set of stimuli while ignoring others. Human research suggests that the binding of diverse stimuli into one attended percept requires phase-locked oscillatory activity in the brain. Even insects display oscillatory brain activity during visual attention tasks, but it is unclear if neural oscillations in insects are selectively correlated to different features of attended objects. We addressed this question by recording local field potentials in the Drosophila central complex, a brain structure involved in visual navigation and decision making. We found that attention selectively increased the neural gain of visual features associated with attended objects and that attention could be redirected to unattended objects by activation of a reward circuit. Attention was associated with increased beta (20- to 30-Hz) oscillations that selectively locked onto temporal features of the attended visual objects. Our results suggest a conserved function for the beta frequency range in regulating selective attention to salient visual features.
The Effect of Sound Lure Frequency and Habitat Type on Male Aedes albopictus (Diptera: Culicidae) Capture Rates With the Male Aedes Sound Trap

Abstract The global distribution of Aedes albopictus (Skuse) is rapidly expanding which has contributed to the emergence and re-emergence of dengue and chikungunya outbreaks. Improvements in vector surveillance are necessary to facilitate optimized, evidence-based vector control operations. Current trapping technology used to target Ae. albopictus and other Aedes species for vector surveillance are limited in both scale and scope, thus novel tools are required. Here, we evaluated the Male Aedes Sound Trap (MAST) for its capacity to sample male Ae. albopictus. Aims of this study were twofold: 1) to determine the most effective frequency for capturing male Ae. albopictus and 2) to investigate fine-scale variations in male Ae. albopictus abundance. MASTs which produced sound lure frequencies between 500 and 650 Hz captured significantly more male Ae. albopictus than those with sound lure frequencies set to 450 Hz. Further, the higher sound lure frequency of 700 Hz significantly reduced catches relative to 650 Hz. MASTs placed in woodland habitats captured significantly more male Ae. albopictus than MASTs placed near houses. These results provide baseline information for optimizing sound lure frequencies and placement of the MAST to sample male Ae. albopictus in remote areas.
Technology and implementation science to forge the future of evidence-based psychotherapies: the PRIDE scale-up study

Objective To report the interim results from the training of providers inevidence-based psychotherapies (EBPs) and use of mobile applications. Design and Setting The Partnerships in Research to Implement and Disseminate Sustainable and Scalable Evidence (PRIDE) study is a cluster-randomised hybrid effectiveness-implementation trial comparing three delivery pathways for integrating comprehensive mental healthcare into primary care in Mozambique. Innovations include the use of EBPs and scaling-up of task-shifted mental health services using mobile applications. Main outcome measures We examined EBP training attendance, certification, knowledge and intentions to deliver each component. We collected qualitative data through rapid ethnography and focus groups. We tracked the use of the mobile applications to investigate early reach of a valid screening tool (Electronic Mental Wellness Tool) and the roll out of the EBPs Participants Psychiatric technicians and primary care providers trained in the EBPs. Results PRIDE has trained 110 EBP providers, supervisors and trainers and will train 279 community health workers in upcoming months. The trainings improved knowledge about the EBPs and trainees indicated strong intentions to deliver the EBP core components. Trained providers began using the mobile applications and appear to identify cases and provide appropriate treatment. Conclusions The future of EBPs requires implementation within existing systems of care with fidelity to their core evidence-based components. To sustainably address the vast mental health treatment gap globally, EBP implementation demands: expanding the mental health workforce by training existing human resources; sequential use of EBPs to comprehensively treat mental disorders and their comorbid presentations and leveraging digital screening and treatment applications.
Resting‐state default mode network connectivity in young individuals with Down syndrome

Down syndrome (DS) is a chromosomal disorder that causes intellectual disability. Few studies have been conducted on functional connectivity using resting‐state fMRI (functional magnetic resonance imaging) signals or more specifically, on the relevant structure and density of the default mode network (DMN). Although data on this issue have been reported in adult DS individuals (age: >45 years), the DMN properties in young DS individuals have not been studied. The aim of this study was to describe the density and structure of the DMN network from fMRI signals in young DS (age: <36 years).
Noncanonical thyroid hormone signaling mediates cardiometabolic effects in vivo

Significance This study changes our understanding of how thyroid hormone acts. Thyroid hormone receptors are considered typical nuclear receptors that bind to DNA and, after binding, alter the expression of their target genes and regulate physiological responses. Nevertheless, we show that thyroid hormone still mediates important physiological effects in mice expressing mutant receptors that cannot bind DNA. These are predominantly linked to energy metabolism and include glucose and triglyceride concentrations, body temperature, locomotor activity, and heart rate. This study provides in vivo evidence that thyroid hormone receptors mediate physiologically relevant effects that are independent of DNA binding and direct activation of gene expression. Thyroid hormone (TH) and TH receptors (TRs) α and β act by binding to TH response elements (TREs) in regulatory regions of target genes. This nuclear signaling is established as the canonical or type 1 pathway for TH action. Nevertheless, TRs also rapidly activate intracellular second-messenger signaling pathways independently of gene expression (noncanonical or type 3 TR signaling). To test the physiological relevance of noncanonical TR signaling, we generated knockin mice with a mutation in the TR DNA-binding domain that abrogates binding to DNA and leads to complete loss of canonical TH action. We show that several important physiological TH effects are preserved despite the disruption of DNA binding of TRα and TRβ, most notably heart rate, body temperature, blood glucose, and triglyceride concentration, all of which were regulated by noncanonical TR signaling. Additionally, we confirm that TRE-binding–defective TRβ leads to disruption of the hypothalamic–pituitary–thyroid axis with resistance to TH, while mutation of TRα causes a severe delay in skeletal development, thus demonstrating tissue- and TR isoform-specific canonical signaling. These findings provide in vivo evidence that noncanonical TR signaling exerts physiologically important cardiometabolic effects that are distinct from canonical actions. These data challenge the current paradigm that in vivo physiological TH action is mediated exclusively via regulation of gene transcription at the nuclear level.