Miracle-dz/UniFAR-FTUs huggingface dataset:
Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks

Abstract The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear DNA position remains unclear. We made use of the prominent structure and well-defined heterochromatic landscape of mouse pericentric chromosome domains as a well-studied example of late replicating constitutive heterochromatin. We established a method to manipulate its nuclear position and evaluated the effect on replication timing, DNA compaction and epigenetic composition. Using time-lapse microscopy, we observed that constitutive heterochromatin, known to replicate during late S-phase, was replicated in mid S-phase when repositioned to the nuclear periphery. Out-of-schedule replication resulted in deficient post-replicative maintenance of chromatin modifications, namely silencing marks. We propose that repositioned constitutive heterochromatin was activated in trans according to the domino model of origin firing by nearby (mid S) firing origins. In summary, our data provide, on the one hand, a novel approach to manipulate nuclear DNA position and, on the other hand, establish nuclear DNA position as a novel mechanism regulating DNA replication timing and epigenetic maintenance.
Scoping Review of Dance for Adults With Fibromyalgia: What Do We Know About It?

Background Fibromyalgia is a chronic disorder characterized by widespread muscular tenderness, pain, fatigue, and cognitive difficulties. Nonpharmacological treatment options, such as physical activity, are important for people with fibromyalgia. There are strong recommendations to support engagement in physical activity for symptom management among adults with fibromyalgia. Dance is a mode of physical activity that may allow individuals with fibromyalgia to improve their physical function, health, and well-being. Dance has the potential to promote improved pain processing while simultaneously providing the health and social benefits of engaging in physical activity that contributes to symptom management and overall function rehabilitation. However, we are unaware of current evidence on dance as a nonpharmacological/physical activity intervention for adults with fibromyalgia. Objective The aims of this study were to understand how dance is used therapeutically by individuals with fibromyalgia; to examine the extent, range and nature of research activity in the area; and to determine the value of undertaking a systematic review of interventions. Methods We used and adapted the Arksey and O’Malley scoping framework. The search strategy involved a comprehensive search of main health and electronic social databases, trial registries and grey literature without language limits. Pairs of reviewers independently screened and extracted data and evaluated the methodological quality of randomized control trials. Results Twenty-one unique records for 13 studies met inclusion criteria; the studies included mostly middle-aged women. Types of dance included were aerobic dance, belly dance, dance movement therapy, biodanza and Zumba. Intervention parameters were different among studies. Frequency varied between one to three times a week; all were done in small group settings. Studies evaluated a variety of outcomes in the symptoms, wellness, psychosocial, physical functioning, balance and fitness categories; no studies evaluated the safety or adverse events systematically which is a major weakness of the literature. Conclusions There are few studies in the field of dance and fibromyalgia, suggesting research is in its infancy but slowly growing. They are of European and South American origin, focusing on female participants and a limited number of dance modes. Because the body of literature is small, of low quality and highly heterogeneous, we concluded that a systematic review of interventions on dance is not warranted at this time.
Effect of Antihypertensive Medication on Cerebral Small Vessel Disease: A Systematic Review and Meta-Analysis

Background and Purpose— Hypertension is an important risk factor for cerebral small vessel disease. We aimed to study the effect of antihypertensive medication (AHM) on the progression of cerebral small vessel disease. Methods— We performed a systematic literature search of electronic databases up to January 30, 2017, for randomized controlled trials on the effect of AHM on ≥1 cerebral small vessel disease magnetic resonance imaging markers (ie, white matter hyperintensities, lacunes, microbleeds, enlarged perivascular spaces, acute small subcortical infarcts, and brain atrophy) after ≥1 year. We performed a random-effects meta-analysis using standardized mean difference. Results— We included 4 trials, including patients with stroke, with diabetes mellitus, and people ≥70 years of age. Patients in the AHM group had less progression of white matter hyperintensity during 28 to 47 months (standardized mean difference, −0.19; 95% confidence interval, −0.32 to −0.06; I2=20%; n=1369). Two trials reported on progression of brain atrophy with conflicting results. None of the trials reported on other cerebral small vessel disease markers. Conclusions— AHM has a protective effect on the progression of white matter hyperintensities, but no effect on brain atrophy. There are no trials on the effect of AHM on lacunes, microbleeds, enlarged perivascular spaces, or acute small subcortical infarcts.
Use of ICM B software for on-line analysis of intracranial and arterial pressures in head-injured patients

Objective. To summarize our experience from the first 2 years of use of the ICMþ software in our Neurocritical Care Unit (NCCU). Materials and methods. Ninety-five head-injured patients (74 males, 21 females), average age 36 years, were managed in the NCCU. Intracranial pressure (ICP) was monitored using Codman intraparenchymal probes and arterial blood pressure (ABP) was measured from the radial artery. Signals were monitored by ICMþ software calculating mean values of ICP, ABP, cerebral perfusion pressure (CPP) and various indices describing pressure reactivity, compensation and vascular waveforms of ICP (pulse amplitude, respiratory, and slow waves), etc. Results. Mean ICP was 17 mmHg, mean CPP was 73 mmHg. Seven patients showed permanent disturbance of cerebral autoregulation (mean pressure reactivity index above 0.3). Pressure reactivity index demonstrated significant U-shape relationship with CPP, suggesting loss of pressure reactivity at too low (CPP < 55 mmHg) and too high CPPs (CPP > 95 mmHg). Mean ICP was inversely correlated with respiratory rate (R 1⁄4 0.46; p < 0.0001; reciprocal model). Conclusion. The new version of ICMþ software proved to be useful clinically in the NCCU. It allows continuous monitoring of pressure reactivity and exploratory analysis of factors implicating intracranial hypertension.
The Relationship Between Preference and Performance Measures of Handedness

There is great debate as to the way in which preference and performance measures of handedness are related. Some suggest that they are separable dimensions (e.g. Porac & Coren, 1981), however a bulk of evidence suggests otherwise (Annett, 1970b; 1976; 1985). The study aimed to discover whether any of three tasks were better captured by the EHI (Oldfield, 1971). Participants completed all three performance tasks and the EHI. Results suggest that performance measures tapping more practiced abilities may be better captured by preference inventories. Implications of the findings and how preference and performance measures might be related are discussed. How performance measures relate to different types of handedness dichotomies derived from the EHI are also discussed.
An Overview of PET Radiochemistry, Part 2: Radiometals

This continuing educational review provides an overview on radiometals used for PET. General aspects of radiometal-based radiotracers are covered, and the most frequently applied metallic PET radionuclides, 68Ga, 89Zr, and 64Cu, are highlighted with a discussion of their strengths and limitations.
Role of Kip2 during early mitosis – impact on spindle pole body separation and chromosome capture

ABSTRACT Mitotic spindle dynamics are regulated during the cell cycle by microtubule motor proteins. In Saccharomyces cerevisiae, one such protein is Kip2p, a plus-end motor that regulates the polymerization and stability of cytoplasmic microtubules (cMTs). Kip2p levels are regulated during the cell cycle, and its overexpression leads to the formation of hyper-elongated cMTs. To investigate the significance of varying Kip2p levels during the cell cycle and the hyper-elongated cMTs, we overexpressed KIP2 in the G1 phase and examined the effects on the separation of spindle pole bodies (SPBs) and chromosome segregation. Our results show that failure to regulate the cMT lengths during G1-S phase prevents the separation of SPBs. This, in turn, affects chromosome capture and leads to the activation of spindle assembly checkpoint (SAC) and causes mitotic arrest. These defects could be rescued by either the inactivation of checkpoint components or by co-overexpression of CIN8, which encodes a motor protein that elongates inter-polar microtubules (ipMTs). Hence, we propose that the maintenance of Kip2p level and cMT lengths during early cell division is important to ensure coordination between SPB separation and chromosome capture by kinetochore microtubules (kMTs). Summary: In S. cerevisiae, the length of cytoplasmic microtubule is kept short by Kip2p function during G1-S phase to allow for separation of SPBs and proper chromosome capture.
Modulating Emotional Experience Using Electrical Stimulation of the Medial‐Prefrontal Cortex: A Preliminary tDCS‐fMRI Study

Implicit regulation of emotions involves medial‐prefrontal cortex (mPFC) regions exerting regulatory control over limbic structures. Diminished regulation relates to aberrant mPFC functionality and psychopathology. Establishing means of modulating mPFC functionality could benefit research on emotion and its dysregulation. Here, we tested the capacity of transcranial direct current stimulation (tDCS) targeting mPFC to modulate subjective emotional states by facilitating implicit emotion regulation.
Pregnancy-Associated Plasma Protein-aa Regulates Photoreceptor Synaptic Development to Mediate Visually Guided Behavior

To guide behavior, sensory systems detect the onset and offset of stimuli and process these distinct inputs via parallel pathways. In the retina, this strategy is implemented by splitting neural signals for light onset and offset via synapses connecting photoreceptors to ON and OFF bipolar cells, respectively. It remains poorly understood which molecular cues establish the architecture of this synaptic configuration to split light-onset and light-offset signals. A mutant with reduced synapses between photoreceptors and one bipolar cell type, but not the other, could reveal a critical cue. From this approach, we report a novel synaptic role for pregnancy-associated plasma protein aa (pappaa) in promoting the structure and function of cone synapses that transmit light-offset information. Electrophysiological and behavioral analyses indicated pappaa mutant zebrafish have dysfunctional cone-to-OFF bipolar cell synapses and impaired responses to light offset, but intact cone-to-ON bipolar cell synapses and light-onset responses. Ultrastructural analyses of pappaa mutant cones showed a lack of presynaptic domains at synapses with OFF bipolar cells. pappaa is expressed postsynaptically to the cones during retinal synaptogenesis and encodes a secreted metalloprotease known to stimulate insulin-like growth factor 1 (IGF1) signaling. Induction of dominant-negative IGF1 receptor expression during synaptogenesis reduced light-offset responses. Conversely, stimulating IGF1 signaling at this time improved pappaa mutants' light-offset responses and cone presynaptic structures. Together, our results indicate Pappaa-regulated IGF1 signaling as a novel pathway that establishes how cone synapses convey light-offset signals to guide behavior. SIGNIFICANCE STATEMENT Distinct sensory inputs, like stimulus onset and offset, are often split at distinct synapses into parallel circuits for processing. In the retina, photoreceptors and ON and OFF bipolar cells form discrete synapses to split neural signals coding light onset and offset, respectively. The molecular cues that establish this synaptic configuration to specifically convey light onset or offset remain unclear. Our work reveals a novel cue: pregnancy-associated plasma protein aa (pappaa), which regulates photoreceptor synaptic structure and function to specifically transmit light-offset information. Pappaa is a metalloprotease that stimulates local insulin-like growth factor 1 (IGF1) signaling. IGF1 promotes various aspects of synaptic development and function and is broadly expressed, thus requiring local regulators, like Pappaa, to govern its specificity.
Physiological Responses during Interval Training with Different Intensities and Duration of Exercise

Zuniga, JM, Berg, K, Noble, J, Harder, J, Chaffin, ME, and Hanumanthu, VS. Physiological responses during interval training with different intensities and duration of exercise. J Strength Cond Res 25(5): 1279-1284, 2011-The purpose of this study was to compare 4 interval training (IT) sessions with different intensities and durations of exercise to determine the effect on mean &OV0312;O2, total &OV0312;O2, and duration of exertion ≥95% maximum power output (MPO), and the effects on biomarkers of fatigue such as blood-lactate concentration (BLC) and rating of perceived exertion. The subjects were 12 recreationally competitive male (n = 7, mean ± SD age = 26.2 ± 3.9 years) and female (n = 5, mean ± SD age = 27.6 ± 4.3 years) triathletes. These subjects performed 4 IT sessions on a cycle ergometer varying in intensity (90 and 100% MPO) and duration of exercise (30 seconds and 3 minutes). This study revealed that IT using 30-second duration intervals (30-30 seconds) allows the athlete to perform a longer session, with a higher total and mean &OV0312;O2 HR and lower BLC than 3-minute durations. Similarly, submaximal exertion at 90% of MPO also allows performing longer sessions with a higher total &OV0312;O2 than 100% intensity. Thus, the results of the present study suggested that to increase the total time at high intensity of exercise and total &OV0312;O2 of a single exercise session performed by the athlete, IT protocols of short durations (i.e., 30 seconds) and submaximal intensities (i.e., 90% MPO) should be selected. Furthermore, performing short-duration intervals may allow the athlete to complete a longer IT session with greater metabolic demands (&OV0312;O2) and lower BLC than longer (i.e., 3 minutes) intervals.
Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

For next‐generation sequencing technologies, sufficient base‐pair coverage is the foremost requirement for the reliable detection of genomic variants. We investigated whether whole‐genome sequencing (WGS) platforms offer improved coverage of coding regions compared with whole‐exome sequencing (WES) platforms, and compared single‐base coverage for a large set of exome and genome samples. We find that WES platforms have improved considerably in the last years, but at comparable sequencing depth, WGS outperforms WES in terms of covered coding regions. At higher sequencing depth (95x–160x), WES successfully captures 95% of the coding regions with a minimal coverage of 20x, compared with 98% for WGS at 87‐fold coverage. Three different assessments of sequence coverage bias showed consistent biases for WES but not for WGS. We found no clear differences for the technologies concerning their ability to achieve complete coverage of 2,759 clinically relevant genes. We show that WES performs comparable to WGS in terms of covered bases if sequenced at two to three times higher coverage. This does, however, go at the cost of substantially more sequencing biases in WES approaches. Our findings will guide laboratories to make an informed decision on which sequencing platform and coverage to choose.
Effect of different media and growth regulators on the in vitro shoot proliferation of aspen, hybrid aspen and white poplar male tree and molecular analysis of variants in micropropagated plants

Among other in vitro factors like temperature and light, concentration of plant growth regulators and medium constituents are two of the most important aspects of successful micropropagation. With the aim of optimization of in vitro multiplication of Populus alba L. , Populus tremula L. and Populus tremula L. x Populus tremuloides Michx , the effect of MS and WPM media with various concentrations of BAP and 2iP was studied. The following multiplication parameters were monitored: number of shoots regenerated/explant, explant height, and explants weight were determined. MS medium proved to be the most effective one, resulting in better and morphologically superior microshoots as compared to WPM medium in the case of Populus alba. However in Populus tremula and Populus tremula x Populus Tremuloides the highest number of shoots was found when grown on WPM medium. In all three poplar lines, the highest shoot multiplication was obtained on MS and Life science journal 2011 8 (1)177-184 Published Research Articles in International Journals 2010-2011 Effect of Gamma Irradiation on Enhancement of Some Economic Traits and Molecular Changes in Hibiscus Sabdariffa L. Fadia El Sherif, Salah Khattab, Ezzat Goniam, Nashwa Salem and Khaled Radwan
Exogenous IL‐6 induces mRNA splice variant MBD2_v2 to promote stemness in TP53 wild‐type, African American PCa cells

African American men (AAM) are at higher risk of being diagnosed with prostate cancer (PCa) and are at higher risk of dying from the disease compared to European American men (EAM). We sought to better understand PCa molecular diversity that may be underlying these disparities. We performed RNA‐sequencing analysis on high‐grade PCa to identify genes showing differential tumor versus noncancer adjacent tissue expression patterns unique to AAM or EAM. We observed that interleukin‐6 (IL‐6) was upregulated in the nonmalignant adjacent tissue in AAM, but in EAM IL‐6 expression was higher in PCa tissue. Enrichment analysis identified that genes linked to the function of TP53 were overrepresented and downregulated in PCa tissue from AAM. These RNA‐sequencing results informed our subsequent investigation of a diverse PCa cell line panel. We observed that PCa cell lines that are TP53 wild‐type, which includes cell lines derived from AAM (MDA‐PCa‐2b and RC77T), did not express detectable IL‐6 mRNA. IL‐6 treatment of these cells downregulated wild‐type TP53 protein and induced mRNA and protein expression of the epigenetic reader methyl CpG binding domain protein 2 (MBD2), specifically the alternative mRNA splicing variant MBD2_v2. Further investigation validated that upregulation of this short isoform promotes self‐renewal and expansion of PCa cancer stem‐like cells (CSCs). In conclusion, this report contributes to characterizing gene expression patterns in high‐grade PCa and adjacent noncancer tissues from EAM and AAM. The results we describe here advance what is known about the biology associated with PCa race disparities and the molecular signaling of CSCs.
From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity

Particulate methane monooxygenase (pMMO) is a copper-dependent integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. Studies of isolated pMMO have been hindered by loss of enzymatic activity upon its removal from the native membrane. To characterize pMMO in a membrane-like environment, we reconstituted pMMOs from Methylococcus (Mcc.) capsulatus (Bath) and Methylomicrobium (Mm.) alcaliphilum 20Z into bicelles. Reconstitution into bicelles recovers methane oxidation activity lost upon detergent solubilization and purification without substantial alterations to copper content or copper electronic structure, as observed by electron paramagnetic resonance (EPR) spectroscopy. These findings suggest that loss of pMMO activity upon isolation is due to removal from the membranes rather than caused by loss of the catalytic copper ions. A 2.7 Å resolution crystal structure of pMMO from Mm. alcaliphilum 20Z reveals a mononuclear copper center in the PmoB subunit and indicates that the transmembrane PmoC subunit may be conformationally flexible. Finally, results from extended X-ray absorption fine structure (EXAFS) analysis of pMMO from Mm. alcaliphilum 20Z were consistent with the observed monocopper center in the PmoB subunit. These results underscore the importance of studying membrane proteins in a membrane-like environment and provide valuable insight into pMMO function.
Out of sight, out of mind: A content analysis on media framing of incarceration

This thesis uses a content analysis in order to answer the question of how incarceration is framed by popular reality and fictional dramas focused on prisons. Employing a coding system to analyze the episodes of two popular televisions show about incarceration, this study is concerned with how and what content is being presented to the audience and how it is framed. Using Oz and Lock-up as text, the study used Entman’s (1993) four processes of framing communication. It was determined that the information and themes of incarceration in the television programs were unrealistic representations of prisoners, rehabilitation programs within the prisons, and reasons for incarceration. The study determined an inaccurate frame of the prison demographic is presented to audiences regarding incarceration. Although this study represents a limited amount of text, the results leave open the possibility of furthering the research and applying the content to a larger-scale study, including the impact of the frames on prison programs and sentencing. Table of
Know Rob 2.0 — A 2nd Generation Knowledge Processing Framework for Cognition-Enabled Robotic Agents

In this paper we present KnowRob2, a second generation knowledge representation and reasoning framework for robotic agents. KnowRob2 is an extension and partial redesign of KnowRob, currently one of the most advanced knowledge processing systems for robots that has enabled them to successfully perform complex manipulation tasks such as making pizza, conducting chemical experiments, and setting tables. The knowledge base appears to be a conventional first-order time interval logic knowledge base, but it exists to a large part only virtually: many logical expressions are constructed on demand from data structures of the control program, computed through robotics algorithms including ones for motion planning and solving inverse kinematics problems, and log data stored in noSQL databases. Novel features and extensions of KnowRob2 substantially increase the capabilities of robotic agents of acquiring open-ended manipulation skills and competence, reasoning about how to perform manipulation actions more realistically, and acquiring commonsense knowledge.