Miracle-dz/UniFAR-FTUs huggingface dataset:
Telomeric DNA localization on dinoflagellate chromosomes: structural and evolutionary implications

Dinoflagellates are eukaryotic microalgae with distinct chromosomes throughout the cell cycle which lack histones and nucleosomes. The molecular organization of these chromosomes is still poorly understood. We have analysed the presence of telomeres in two evolutionarily distant and heterogeneous dinoflagellate species (Prorocentrum micans and Amphidinium carterae) by FISH with a probecontaining the Arabidopsis consensus telomeric sequence. Telomere structures were identified at the chromosome ends of both species during interphase and mitosis and were frequently associated with the nuclear envelope. These results identify for the first time telomere structures in dinoflagellate chromosomes, which are formed in the absence of histones. The presence of telomeres supports the linear nature of dinoflagellate chromosomes.
Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish

As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one‐third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine‐scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.
Simulating Transcranial Direct Current Stimulation With a Detailed Anisotropic Human Head Model

Transcranial direct current stimulation (tDCS) is a noninvasive brain stimulation technique able to induce long-lasting changes in cortical excitability that can benefit cognitive functioning and clinical treatment. In order to both better understand the mechanisms behind tDCS and possibly improve the technique, finite element models are used to simulate tDCS of the human brain. With the detailed anisotropic head model presented in this study, we provide accurate predictions of tDCS in the human brain for six of the practically most-used setups in clinical and cognitive research, targeting the primary motor cortex, dorsolateral prefrontal cortex, inferior frontal gyrus, occipital cortex, and cerebellum. We present the resulting electric field strengths in the complete brain and introduce new methods to evaluate the effectivity in the target area specifically, where we have analyzed both the strength and direction of the field. For all cerebral targets studied, the currently accepted configurations produced sub-optimal field strengths. The configuration for cerebellum stimulation produced relatively high field strengths in its target area, but it needs higher input currents than cerebral stimulation does. This study suggests that improvements in the effects of transcranial direct current stimulation are achievable.
Procedures for estimating seismic permanent displacements on tailings storage facilities and mine waste dumps

The use of pseudo-static procedures for assessing seismic slope stability analysis of a tailings storage facility (TSF) and a mine waste dump (MWD) is a common practice in geotechnical engineering; however, new methodologies have emerged for the calculation of seismic induced permanent displacements of earth structures, which is considered a more reliable approach compared to the calculation of a factor of safety (FOS) obtained by the pseudo-static procedure. The authors have studied the application of several methodologies to assess the seismic stability of TSF and MWD based on two case studies. One-dimensional (1D) nonlinear seismic response and slope stability analyses were performed as part of these applications. Cyclic laboratory tests on coarse tailings and mine waste were performed to evaluate their dynamic properties and were compared to current state-of-practice literature curves. The resulting displacements using these procedures proved, in general, to be similar. This research suggests that the seismic analysis should be less focused on the pseudo-static FOS as a parameter to predict the seismic stability of TSF and MWD, unless a rational criterion is chosen for the determination of the seismic coefficient.
Application of Parallel Factor Analysis (PARAFAC) to electrophysiological data

The identification of important features in multi-electrode recordings requires the decomposition of data in order to disclose relevant features and to offer a clear graphical representation. This can be a demanding task. Parallel Factor Analysis (PARAFAC; Hitchcock, 1927; Carrol and Chang, 1970; Harshman, 1970) is a method to decompose multi-dimensional arrays in order to focus on the features of interest, and provides a distinct illustration of the results. We applied PARAFAC to analyse spatio-temporal patterns in the functional connectivity between neurons, as revealed in their spike trains recorded in cat primary visual cortex (area 18). During these recordings we reversibly deactivated feedback connections from higher visual areas in the pMS (posterior middle suprasylvian) cortex in order to study the impact of these top-down signals. Cross correlation was computed for every possible pair of the 16 electrodes in the electrode array. PARAFAC was then used to reveal the effects of time, stimulus, and deactivation condition on the correlation patterns. Our results show that PARAFAC is able to reliably extract changes in correlation strength for different experimental conditions and display the relevant features. Thus, PARAFAC proves to be well-suited for the use in the context of electrophysiological (action potential) recordings.
Diffuse optical spectroscopic imaging correlates with final pathological response in breast cancer neoadjuvant chemotherapy

Diffuse optical spectroscopic imaging (DOSI) non-invasively and quantitatively measures tissue haemoglobin, water and lipid. Pilot studies in small groups of patients demonstrate that DOSI may be useful for longitudinal monitoring and predicting breast cancer neoadjuvant chemotherapy pathological response. This study evaluates the performance of a bedside DOSI platform in 34 breast cancer patients followed for several months. DOSI optical endpoints obtained at multiple timepoints are compared with final pathological response. Thirty-six stage II/III breast cancers (34 patients) were measured in vivo with DOSI prior to, in the middle of and after the completion of pre-surgical neoadjuvant chemotherapy. Cancer therapies ranged from standard anthracyclines to targeted therapies. Changes in DOSI-measured parameters at each timepoint were compared against final surgical pathology. Absolute changes in the tumour-to-normal (T/N) ratio of tissue deoxyhaemoglobin concentration (ctHHb) and relative changes in the T/N ratio of a tissue optical index (TOI) were most sensitive and correlate to pathological response. Changes in ctHHb and TOI were significantly different between tumours that achieved pathological complete response (pCR) versus non-pCR. By therapy midpoint, mean TOI-T/N changes were 47±8 versus 20±5 per cent for pCR versus non-pCR subjects, respectively (Z=0.011). Changes in ctHHb and TOI scaled significantly with the degree of pathological response (non-, partial and complete). DOSI measurements of TOI separated pCR from non-pCR by therapy midpoint regardless of drug or dosing strategy. This approach is well suited to monitoring breast tumour response and may provide feedback for optimizing therapeutic outcomes and minimizing side-effects.
Effects of Subanesthetic Concentrations of Isoflurane and Their Interactions with Epinephrine on Acquisition and Retention of the Rabbit Nictitating Membrane Response

BackgroundEvidence concerning the concentrations of volatile anesthetics that prevent learning and recall is limited. Epinephrine is believed to enable learning during anesthesia. We investigated the effects of Isoflurane and its interaction with epinephrine on learning and subsequent retention of the rabbit's classically conditioned nictitating membrane response. MethodsIn experiment 1, a tone (conditioned stimulus, CS) preceded paraorbital shock (unconditioned stimulus, US) during 60-min daily sessions of 60 presentations of these paired stimuli for 6 days of acquisition training under 0, 0.4%, or 0.8% isoflurane (n = 8, 13, and 9, respectively). Responses were recorded as conditioned responses (CRs) if they occurred during the CS and before the onset of the US. After 1 day of rest, the animals were given 3 days of extinction consisting of 60 presentations of CS-alone and without Isoflurane to assess the retention of CRs from acquisition training. In experiment 2, epinephrine In a dose of 0, 0.01, or 0.1 mg/kg was Injected subcutaneously in rabbits receiving 0.4% isoflurane. Two types of epinephrine were used, a sustained release form and epinephrine hydrochloride. Acquisition and retention were tested in the same way as in experiment 1. No isoflurane or epinephrine was used during retention testing. ResultsLearning was significantly suppressed during 0.4% isoflurane (≊0.2 MAC) treatment and eliminated during 0.8% (≊0.4 MAC). Information learned during administration of 0.4% isoflurane was not retained (P < 0.05). Although the low dose of epinephrine improved learning during the last day of the acquisition phase (P < 0.05), there were no differences between the treatment groups on any of the remaining acquisition or extinction days. ConclusionsThere was no learning during treatment with 0.8% concentration. Even a 0.4% concentration, which allowed some learning, abolished CRs in extinction, perhaps because of state-dependent retrieval. Epinephrine did not alter substantially the rates of CR acquisition or resistance to extinction.
Experimental investigation of sagging and ballooning for a completely voided pressure tube of Indian PHWR under heatup condition

In a nuclear reactor Loss of Coolant accident (LOCA) considers wide range of postulated damage or rupture of pipe in the heat transport piping system. In the case of LOCA with/without failure of emergency core cooling system in a Pressurised Heavy Water Reactor (PHWR), the Pressure Tube (PT) temperature could rise significantly due to fuel heat up and gross mismatch of the heat generation and heat removal in the affected channel. The extent and nature of deformation is important from reactor safety point of view. Experimental set-ups have been designed and fabricated to simulate sagging (downward deformation) and ballooning (radial deformation) of PT for 220 MWe Indian PHWRs. Experiments are conducted both for sagging and ballooning of voided PTs. It is observed that sagging initiates at a temperature around 450�C. The complete contact between PT and Calandria Tube (CT) occurs at around 585C. At 60 bar internal pressure and initial heat up rate of 2.37C/sec, ballooning of PT initiates at a temperature around 520�C. The PT-CT contact is found to take place at 640C temperature and strain rates is found to be 0.125% per second. The structural integrity of PT is retained (no breach) for all the experiments. The PT heatup is found to be arrested after the contact between PT and CT, thus establishing moderator acting as an efficient heat sink for IPHWRs. Keywords—Pressure Tube, Calandria Tube, Thermo-mechanical deformation, Boiling heat transfer, Reactor safety
THE SEROLOGIC SPECIFICITY OF TROPOCOLLAGEN TELOPEPTIDES

Tropocollagen preparations from carp, buffalo fish, rats, calves, sheep, and humans have been studied by electron microscopy and serologic methods. Tropocollagens from each species appeared identical by electron microscopy but they were readily distinguished (except between sheep and calves) by C'-fixation tests with rabbit antisera against the various tropocollagens. Tests with calf tropocollagen antiserum showed no distinction between tropocollagen isolated from different tissues nor between individuals of the same or different strains. The major immunogenic sites in native tropocollagen are the telopeptides, and these are present on both α1- and α2-chains. The C'-fixing activity was lost with heat denaturation of the tropocollagen, but could be recovered in a concentration-dependent process on cooling. The fact that pure and enzyme-treated collagen can provoke serologic reaction implies that collagenous sutures and prostheses used in surgery may lead to sensitization and rejection, a fact which may merit clinical concern.
Temperature-sensitive heparin-modified poloxamer hydrogel with affinity to KGF facilitate the morphologic and functional recovery of the injured rat uterus

Abstract Endometrial injury usually results in intrauterine adhesion (IUA), which is an important cause of infertility and recurrent miscarriage in reproductive women. There is still lack of an effective therapeutic strategy to prevent occurrence of IUA. Keratinocyte growth factor (KGF) is a potent repair factor for epithelial tissues. Here, a temperature-sensitive heparin-modified poloxamer (HP) hydrogel with affinity to KGF (KGF-HP) was used as a support matrix to prevent IUA and deliver KGF. The rheology of KGF-HP hydrogel was carefully characterized. The cold KGF-HP solution was rapidly transited to hydrogel with suitable storage modulus (G′) and loss modulus (G″) for the applications of uterus cavity at temperature of 33 °C. In vitro release demonstrated that KGF was released from HP hydrogels in sustained release manner for a long time. In vivo bioluminescence imaging showed that KGF-HP hydrogel was able to prolong the retention of the encapsulated KGF in injured uterus of rat model. Moreover, the morphology and function of the injured uterus were significantly recovered after administration of KGF-HP hydrogel, which were evaluated by two-dimensional ultrasound imaging and receptive fertility. Not only proliferation of endometrial glandular epithelial cells and luminal epithelial cells but also angiogenesis of injured uterus were observed by Ki67 and CD31 staining after 7 d of treatment with KGF-HP hydrogel. Finally, a close relatively relationship between autophagy and proliferation of endometrial epithelial cells (EEC) and angiogenesis was firstly confirmed by detecting expression of LC3-II and P62 after KGF treatment. Overall, KGF-HP may be used as a promising candidate for IUA treatment.
An analysis of the indicators affecting urban household food insecurity in the informal settlement area of the Cape Town Metropole

Households in the informal settlement areas of the Cape Town Metropole face different challenges in terms of poverty and food security. Challenges are determined by the social and economic circumstances these households subside in. Many initiatives by the Western Cape Department of Agriculture was initiated to aid households in these areas. Some of the initiatives include the implementation of urban household and community food gardens assisted by the Department’s extension division. A thorough analysis of these indicators is imperative to initiate development planning. The results showed that 26.1% of household heads completed school, while 33.8% did not reach secondary school (grade 7). The average household size is 4.29 persons in the study area. The average age of household head was 48 and 50.64 years for non-farmer groups and urban farming households respectively. The average monthly income per household was R3543.22. The main source of income generated throughout the year derived from formal salaries or wages (46.4%), while child support grants and pension funds also contributed towards income. Expenditure factors accounts for 20.4% of the variance of factors affecting food security. The expenditure component is comprised by the share of food expenditure on income, the total value of food consumed and the household diet diversity score. The socio-economic indicators component forms the second largest component group (15.15%), while the components with a lesser effect include a food security component, an urban farming component and a geographical and market component. Keywords: Urban Agriculture, household gardens, community gardens, food security, household size, age, gender, education level, migrant workers, household income
Who’s Hungry: The Development of a Youth Guide

This study addresses the development of a Youth Guide to hunger in the Greater Toronto Area (GTA). The initial Youth Guide was created to address the senstive topics of local hunger and poverty in a format that would be accessible to both students and teachers. Following an in depth review of historical constructions of the poor, as well as ideological assumptions, the decision was made to re-evaluate the initial Youth Guide, and reconstruct it. The re-evaluation included a critique of the overall content, tone and, layout of the existing Youth Guide with a view to designing an updated “unbiased” version for 2009. A review of the historical construction of “the poor” also informed the construction of the revised document. Revisions were made to the 2008 Youth Guide to create an improved 2009 Youth Guide to Hunger in the GTA, which is Chapter 4. Further reflections regarding the creation of documents of a sensitive nature are suggested and reviewed for future publications.
The Occurrence of Veterinary Pharmaceuticals in the Environment: A Review

It is well known that there is a widespread use of veterinary pharmaceuticals and consequent release into different ecosystems such as freshwater bodies and groundwater systems. Furthermore, the use of organic fertilizers produced from animal waste manure has been also responsible for the occurrence of veterinary pharmaceuticals in agricultural soils. This article is a review of different studies focused on the detection and quantification of such compounds in environmental compartments using different analytical techniques. Furthermore, this paper reports the main challenges regarding veterinary pharmaceuticals in terms of analytical methods, detection/quantification of parent compounds and metabolites, and risks/toxicity to human health and aquatic ecosystems. Based on the existing literature, it is clear that only limited data is available regarding veterinary compounds and there are still considerable gaps to be bridged in order to remediate existing problems and prevent future ones. In terms of analytical methods, there are still considerable challenges to overcome considering the large number of existing compounds and respective metabolites. A number of studies highlight the lack of attention given to the detection and quantification of transformation products and metabolites. Furthermore more attention needs to be given in relation to the toxic effects and potential risks that veterinary compounds pose to environmental and human health. To conclude, the more research investigations focused on these subjects take place in the near future, more rapidly we will get a better understanding about the behavior of these compounds and the real risks they pose to aquatic and terrestrial environments and how to properly tackle them.
Assessment of objective quality measures for speech intelligibility

This paper assesses 9 prominent objective quality measures for their potential in intelligibility estimation. Degradation considered include additive noises and those introduced by coding and enhancement schemes, totalling 78 types. This paper is believed to be the first to conduct an assessment on such a large combination of quality measures and degradations allowing side-byside analysis. Experimental results show that the sophisticated perceptual-based measures which are superior for quality estimation, do not necessarily correlate well with human intelligibility and, in fact, give poorer correlations when enhancement schemes are considered. Meanwhile, the weighted spectral slope (WSS) emerges to be the most promising approach among all measures considered, scoring the highest correlation in 5 out of the 6 test sets. Worth noting are the positive correlations obtained with WSS which range from 0.14 to 0.86, as opposed to those with PESQ from -0.58 to 0.74. Such findings put WSS, a relatively conventional measure, in a new light as a potential intelligibility assessor.
bcl‐2 expression in epidermal keratinocytic diseases

Background. The bcl‐2 protein has been shown to suppress apoptosis, and overexpression of the bcl‐2 protein has been reported in several malignant tumors. Skin is one of the largest organs in the body, and the most common human malignancies arise from keratinocytes in the epidermis. In this paper, the authors analyzed immunohistochemically the expression of the bcl‐2 protein in several keratinocytic (KC) tumors and inflammatory skin disorders to investigate the role of bcl‐2 in the development of benign and malignant skin tumors.
Concise Review: Are Stimulated Somatic Cells Truly Reprogrammed into an ES/iPS-Like Pluripotent State? Better Understanding by Ischemia-Induced Multipotent Stem Cells in a Mouse Model of Cerebral Infarction

Following the discovery of pluripotent stem (PS) cells such as embryonic stem (ES) and induced pluripotent stem (iPS) cells, there has been a great hope that injured tissues can be repaired by transplantation of ES/iPS-derived various specific types of cells such as neural stem cells (NSCs). Although PS cells can be induced by ectopic expression of Yamanaka's factors, it is known that several stimuli such as ischemia/hypoxia can increase the stemness of somatic cells via reprogramming. This suggests that endogenous somatic cells acquire stemness during natural regenerative processes following injury. In this study, we describe whether somatic cells are converted into pluripotent stem cells by pathological stimuli without ectopic expression of reprogramming factors based on the findings of ischemia-induced multipotent stem cells in a mouse model of cerebral infarction.