Miracle-dz/UniFAR-FTUs huggingface dataset:
Seed dormancy and germination vary within and among species of milkweeds

Declines in pollinator populations and monarch butterflies require restoration of habitats with the plants and floral resources that support them. Monarch butterflies in particular lay their eggs exclusively on milkweed species, which their caterpillars require as a food source. Restoring populations of milkweeds can involve planting plugs grown from seed, but recommendations for breaking dormancy and germinating milkweed seeds often disagree. We tested the hypothesis that seed germination and dormancy vary within and among species of milkweed, and found substantial differences across species, and even between populations of the same milkweeds.
Dipeptide-induced Cl-secretion in proximal tubule cells.

During a survey of dipeptides that might be transported by the renal PEPT2 transporter in proximal tubule cells, we discovered that acidic dipeptides could stimulate transient secretory anion current and conductance increases in intact cell monolayers. The stimulatory effect of acidic dipeptides was observed in several proximal tubule cell lines that have been recently developed by immortalization of early proximal tubule primary cultures from the Wistar-Kyoto and spontaneously hypertensive rat strains and humans, suggesting that this phenomenon is a characteristic of proximal tubule cells. The electrical current induced in intact monolayers by Ala-Asp, a representative of these acidic dipeptides, must represent Cl- secretion rather than Na+ or H+ absorption, because 1) it was Na+ independent, 2) it showed a pH dependence different from that of the PEPT2 cotransporter, and 3) it correlated with an Ala-Asp-induced increase in Cl- conductance of the apical membrane in basolaterally amphotericin B-permeabilized monolayers. The secretory current could be inhibited by stilbene disulfonates, but not diphenylamine-2-carboxylates, suggesting a non-cystic fibrosis transmembrane conductance regulator type of Cl- conductance. The effect of Ala-Asp was dose dependent, with an apparent 50% effective concentration of ∼1 mM. Ala-Asp also produced intracellular acidification, suggesting that acidic dipeptides are also substrates for an H+-peptide cotransporter.
HIV infection is influenced by dynamin at 3 independent points in the viral life cycle

CD4 T cells are important cellular targets for HIV‐1, yet the primary site of HIV fusion remains unresolved. Candidate fusion sites are either the plasma membrane or from within endosomes. One area of investigation compounding the controversy of this field, is the role of the protein dynamin in the HIV life cycle. To understand the role of dynamin in primary CD4 T cells we combined dynamin inhibition with a series of complementary assays based on single particle tracking, HIV fusion, detection of HIV DNA products and active viral transcription. We identify 3 levels of dynamin influence on the HIV life cycle. Firstly, dynamin influences productive infection by preventing cell cycle progression. Secondly, dynamin influences endocytosis rates and increases the probability of endosomal fusion. Finally, we provide evidence in resting CD4 T cells that dynamin directly regulates the HIV fusion reaction at the plasma membrane. We confirm this latter observation using 2 divergent dynamin modulating compounds, one that enhances dynamin conformations associated with dynamin ring formation (ryngo‐1‐23) and the other that preferentially targets dynamin conformations that appear in helices (dyngo‐4a). This in‐depth understanding of dynamin's roles in HIV infection clarifies recent controversies and furthermore provides evidence for dynamin regulation specifically in the HIV fusion reaction.
Coping, resilience and posttraumatic growth among Eritrean female refugees living in Norwegian asylum reception centres: A qualitative study

Background: The links between migration and health are well documented. Being a refugee exacerbates migrants’ vulnerability through trauma and loss. The aim of this study is to identify sources of resilience, coping and posttraumatic growth in female Eritrean refugees living in Norwegian asylum reception centres. Method: The study had a qualitative, descriptive and explorative design with two focus group interviews and 10 individual in-depth interviews. Participants included 18 female Eritrean refugees aged 18–60, who had obtained refugee status and were still living in an asylum reception centre. A content-focused hermeneutic analytic approach was used. Results: Interviewees described the challenges of pre-flight and flight trauma, conditions at the refugee centre, communication difficulties and the ‘endless’ waiting for transfer to a municipality. To cope, they found it helpful to focus on the future and to think positively. Fellowship with and support from fellow Eritrean refugees were essential as they became a proxy family and provided a strong ethnic identity. Their religious belief also helped them cope and gave them hope for the future. Discussion: The interviewees in this study perceived their psychological problems as a normal reaction to what they had been through. Religious belief was an important resilience factor, as was social support, especially from peers. Conclusion: The interviewees’ coping was based on the realization of their psychological reactions being normal while doing their utmost to focus on their aims and hopes for the future.
Load Balancing for 5G Ultra-Dense Networks Using Device-to-Device Communications

Load balancing is an effective approach to address the spatial–temporal fluctuation problem of mobile data traffic for cellular networks. The existing schemes that focus on channel borrowing from neighboring cells cannot be directly applied to the future 5G wireless networks, because the neighboring cells will reuse the same spectrum band in 5G systems. In this paper, we consider an orthogonal frequency division multiple access ultra-dense small cell network, where device-to-device (D2D) communication is advocated to facilitate load balancing without extra spectrum. Specifically, the data traffic can be effectively offloaded from a congested small cell to other underutilized small cells by D2D communications. The problem is naturally formulated as a joint resource allocation and D2D routing problem that maximizes the system sum-rate. To efficiently solve the problem, we decouple the problem into a resource allocation subproblem and a D2D routing subproblem. The two subproblems are solved iteratively as a monotonic optimization problem and a complementary geometric programming problem, respectively. Simulation results show that the data sum-rate in the neighboring small cells increases 20% on average by offloading the data traffic in the congested small cell to the neighboring small cell base stations.
A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network

Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.
THiCweed: fast, sensitive detection of sequence features by clustering big datasets

We present THiCweed, a new approach to analyzing transcription factor binding data from high-throughput chromatin-immunoprecipitation-sequencing (ChIP-seq) experiments. THiCweed clusters bound regions based on sequence similarity using a divisive hierarchical clustering approach based on sequence similarity within sliding windows, while exploring both strands. ThiCweed is specially geared towards data containing mixtures of motifs, which present a challenge to traditional motif-finders. Our implementation is significantly faster than standard motif-finding programs, able to process 30,000 peaks in 1-2 hours, on a single CPU core of a desktop computer. On synthetic data containing mixtures of motifs it is as accurate or more accurate than all other tested programs. THiCweed performs best with large “window” sizes (≥ 50bp), much longer than typical binding sites (7-15 base pairs). On real data it successfully recovers literature motifs, but also uncovers complex sequence characteristics in flanking DNA, variant motifs, and secondary motifs even when they occur in < 5% of the input, all of which appear biologically relevant. We also find recurring sequence patterns across diverse ChIP-seq data sets, possibly related to chromatin architecture and looping. THiCweed thus goes beyond traditional motif-finding to give new insights into genomic TF binding complexity.
Nuclear epidemiologic studies and the estimation of DREF

Abstract Purpose: Estimating cancer risks for continuous radiation exposures based upon data from acute exposures has been an important public health problem. A dose and dose rate effectiveness factor (DDREF) is typically used to estimate cancer risks for chronic exposures based upon risk estimates from acute exposures. A value of 2 for a DDREF has most often been used as proposed by the ICRP in ICRP60; however, an influential analysis of several cohorts concluded that there is no risk difference between acute and chronic exposures. It is the purpose of this article to analyze the recent nuclear worker studies and estimate the dose rate effectiveness factor, DREF, for solid cancers. Materials and methods: Twelve mortality studies were identified each with at least 100 cancer deaths and a meta-analysis was then carried out using their individual ratio of low dose rate cancer effect (LDR) to the corresponding high dose rate effect from the A-bomb cohort (LSS). The ratio is denoted by Q and its reciprocal is then an estimate of the DREF. Results: The result was Q= 0.36 (95% CI = 0.11, 0.60) and DREF = 2.63 (95% confidence interval [CI] = 1.61, 7.14). Clearly, this estimate is more consistent with a DREF of 2 than with a DREF of 1. The difficulty with the estimate Q = 0.36 is that it is driven by only two large and dissimilar worker studies, the INWORKS study (q1 = 1.14) and the Mayak worker cohort (q3 = 0.30). The higher exposures for these nuclear workers were often in the early years (e.g. before 1960) with exposures from neutrons and internal emitters that are not included in the risk analyses resulting in likely overestimation of cancer effects per dose which would increase the estimate of the DREF. The Mayak study did, however, adjust for plutonium exposures. Finally, consideration is given to other cohort studies where DREF values may possibly be determined, such as the environmental exposures to the Techa River area residents and the Chernobyl cleanup workers as well as medical X-ray workers. Although dissimilar an overall meta-analysis yielded a Q = 0.45 (95% CI = 0.24, 0.66). Conclusions: It is concluded that the best estimate of a DREF is still about 2. However, because of the various problems with the epidemiology studies, especially their dosimetry, it is concluded that a DREF of about 2 should be accepted with considerable caution since it is driven solely by the Mayak study.
Progress in the development of anthropomorphic fluidic hands for a humanoid robot

New lightweight anthropomorphic hands are presented for application in a humanoid robot. These hands possess 13 to 15 degrees of freedom and are driven by flexible fluidic actuators that are integrated in the finger joints. The compact design of the hands contains a pressure unit that is housed in the metacarpus. Alternatively, the pressure unit can be mounted externally, which leads to a further mass reduction. The new design and its performance shall be described in the present article.
TENSIPRESSER PRECISION IN MEASURING COOKED RICE ADHESIVENESS

Precision in measuring cooked rice adhesiveness was studied using a Tensipresser and the “full cup” method. To determine the optimum adhesiveness parameter, 14 samples each from rice harvests in 1992 and 1993 were used. Out of the 42 parameters derived from a force-distance curve, the ratio of cumulative adhesiveness to cumulative hardness, was used as the optimum because of its high correlation (r >0.9) with sensory adhesiveness, high precision (mean coefficient of variation (CV) of 14 samples <15% and maximum CV of 14 samples <25 %), and high resolution based on Kruskal-Wallis test statistic H. For parameter , the maximum CV decreased with the increasing number of bites, and statistic H indicated that increasing the number of bites from 1 to 5 increased resolution, but bites exceeding 5 did not clearly do so.
Adaptive Multitemporal SAR Image Filtering Based on the Change Detection Matrix

This letter presents an adaptive filtering approach of synthetic aperture radar (SAR) image times series based on the analysis of the temporal evolution. First, change detection matrices (CDMs) containing information on changed and unchanged pixels are constructed for each spatial position over the time series by implementing coefficient of variation (CV) cross tests. Afterward, the CDM provides for each pixel in each image an adaptive spatiotemporal neighborhood, which is used to derive the filtered value. The proposed approach is illustrated on a time series of 25 ascending TerraSAR-X images acquired from November 6, 2009 to September 25, 2011 over the Chamonix-Mont-Blanc test-site, which includes different kinds of change, such as parking occupation, glacier surface evolution, etc.
Fourier transform (FT)-artifacts and power-function resolution filter in Fourier transform mass spectrometry.

RATIONALE Peak picking algorithms in mass spectrometry face the challenge of picking the correct signals from a mass spectrum. In some cases signal wiggles (side lobes) are also chosen in the produced mass list as if they were real signals. Constraints which are defined in such algorithms do not always guarantee wiggle-free accurate mass list generation out of raw mass spectra. This problem intensifies with acquisitions, which are accompanied by longer transients. Thus, the problem represents a contemporary issue, which propagates with modern high-memory digitizers and exists in both MS and MS/MS spectra. METHODS A solariX FTMS mass spectrometer with an Infinity ICR cell (Bruker Daltonics, Bremen, Germany) coupled to a 12 Tesla magnet (Magnex, UK) was used for the experimental study. Time-domain transients of several different data point lengths 512k, 1M, 2M, 4M, 8M were obtained and were Fourier-transformed to obtain frequency spectra which show the effect of the transient truncation on sinc wiggle developments in FT-ICR-MS. MATLAB simulations were also performed to investigate the origin of the Fourier transform (FT)-artifacts. RESULTS A new filter has been developed to identify and remove FT-artifacts (sinc side lobes) from both frequency and mass spectra. The newly developed filter is based on distinguishing between the FWHM of the correct frequency/mass signals and the FWHM of their corresponding wiggles. The filter draws a reliable confidence limit of resolution range, within which a correct frequency/mass signal is identified. The filter is applicable over a wide mass range of metabolic interest (100-1200 amu). CONCLUSIONS The origin of FT-artifacts due to time-domain transient truncations was thoroughly investigated both experimentally and by simulations in this study. A new solution for this problem with automatic recognition and elimination of these FT-artifacts (side lobes/wiggles) is provided, which is independent of any intensity thresholds, magnetic field strengths and time-domain transient lengths.
Role of cAMP and calcium influx in endothelin-1-induced ANP release in rat cardiomyocytes.

The mechanism of endothelin-1 (ET-1)-induced atrial natriuretic peptide (ANP) release was studied in neonatal rat ventricular cardiomyocytes. These cells expressed a single high-affinity class of ETAreceptor (dissociation constant = 54 ± 18 pM, n = 3), but no ETB receptors. Incubation of cardiomyocytes with ET-1 led to concentration-dependent ANP release and prostacyclin production. ET-1-induced ANP release was affected by neither protein kinase C (PKC) inhibition or downregulation nor by cyclooxygenase inhibition, indicating that ET-1-stimulated ANP secretion is not a PKC-mediated, prostaglandin-dependent process. Furthermore, ET-1 significantly stimulated adenosine 3',5'-cyclic monophosphate (cAMP) production and increased cytosolic calcium concentration in these preparations. Both ET-1-induced calcium influx and ANP release were decreased by the cAMP antagonist Rp-cAMPS, the Rp diastereoisomer of cAMP. Moreover, ET-1-induced ANP secretion was strongly inhibited in the presence of nifedipine as well as in the absence of extracellular calcium. Thus our results suggest that ET-1 stimulates ANP release in ventricular cardiomyocytes via an ETAreceptor-mediated pathway involving cAMP formation and activation of a nifedipine-sensitive calcium channel.
A Critical Role for the Nucleus Reuniens in Long-Term, But Not Short-Term Associative Recognition Memory Formation

Recognition memory for single items requires the perirhinal cortex (PRH), whereas recognition of an item and its associated location requires a functional interaction among the PRH, hippocampus (HPC), and medial prefrontal cortex (mPFC). Although the precise mechanisms through which these interactions are effected are unknown, the nucleus reuniens (NRe) has bidirectional connections with each regions and thus may play a role in recognition memory. Here we investigated, in male rats, whether specific manipulations of NRe function affected performance of recognition memory for single items, object location, or object-in-place associations. Permanent lesions in the NRe significantly impaired long-term, but not short-term, object-in-place associative recognition memory, whereas single item recognition memory and object location memory were unaffected. Temporary inactivation of the NRe during distinct phases of the object-in-place task revealed its importance in both the encoding and retrieval stages of long-term associative recognition memory. Infusions of specific receptor antagonists showed that encoding was dependent on muscarinic and nicotinic cholinergic neurotransmission, whereas NMDA receptor neurotransmission was not required. Finally, we found that long-term object-in-place memory required protein synthesis within the NRe. These data reveal a specific role for the NRe in long-term associative recognition memory through its interactions with the HPC and mPFC, but not the PRH. The delay-dependent involvement of the NRe suggests that it is not a simple relay station between brain regions, but, rather, during high mnemonic demand, facilitates interactions between the mPFC and HPC, a process that requires both cholinergic neurotransmission and protein synthesis. SIGNIFICANCE STATEMENT Recognizing an object and its associated location, which is fundamental to our everyday memory, requires specific hippocampal–cortical interactions, potentially facilitated by the nucleus reuniens (NRe) of the thalamus. However, the role of the NRe itself in associative recognition memory is unknown. Here, we reveal the crucial role of the NRe in encoding and retrieval of long-term object-in-place memory, but not for remembrance of an individual object or individual location and such involvement is cholinergic receptor and protein synthesis dependent. This is the first demonstration that the NRe is a key node within an associative recognition memory network and is not just a simple relay for information within the network. Rather, we argue, the NRe actively modulates information processing during long-term associative memory formation.
Economic evaluation of a mentorship and enhanced supervision program to improve quality of integrated management of childhood illness care in rural Rwanda

Background Integrated management of childhood illness (IMCI) can reduce under-5 morbidity and mortality in low-income settings. A program to strengthen IMCI practices through Mentorship and Enhanced Supervision at Health centers (MESH) was implemented in two rural districts in eastern Rwanda in 2010. Methods We estimated cost per improvement in quality of care as measured by the difference in correct diagnosis and correct treatment at baseline and 12 months of MESH. Costs of developing and implementing MESH were estimated in 2011 United States Dollars (USD) from the provider perspective using both top-down and bottom-up approaches, from programmatic financial records and site-level data. Improvement in quality of care attributed to MESH was measured through case management observations (n = 292 cases at baseline, 413 cases at 12 months), with outcomes from the intervention already published. Sensitivity analyses were conducted to assess uncertainty under different assumptions of quality of care and patient volume. Results The total annual cost of MESH was US$ 27,955.74 and the average cost added by MESH per IMCI patient was US$1.06. Salary and benefits accounted for the majority of total annual costs (US$22,400 /year). Improvements in quality of care after 12 months of MESH implementation cost US$2.95 per additional child correctly diagnosed and $5.30 per additional child correctly treated. Conclusions The incremental costs per additional child correctly diagnosed and child correctly treated suggest that MESH could be an affordable method for improving IMCI quality of care elsewhere in Rwanda and similar settings. Integrating MESH into existing supervision systems would further reduce costs, increasing potential for spread.
Hemispheric Lateralization of Resting-State Functional Connectivity of the Anterior Insula: Association with Age, Gender, and a Novelty-Seeking Trait

Abstract Resting-state functional connectivity (rsFC) is widely used to examine cerebral functional organization. The imaging literature has described lateralization of insula activations during cognitive and affective processing. Evidence appears to support a role of the right-hemispheric insula in attentional orientation to salient stimulus, interoception, and physiological arousal, and a role of the left-hemispheric insula in cognitive and affective control, as well as perspective taking. In this study, in a large data set of healthy adults, we examined lateralization of the rsFC of the anterior insula (AI) by computing a laterality index (LI) of connectivity with 54 regions from the Automated Anatomic Labeling atlas. At a corrected threshold (p < 0.001), the AI is left lateralized in connectivity with the dorsomedial prefrontal cortex, superior frontal gyrus, inferior frontal cortex, and posterior orbital gyrus and right lateralized in connectivity with the postcentral gyrus, supramarginal gyrus, and superior parietal lobule. In gender differences, women, but not men, showed right-lateralized connectivity to the thalamus. Furthermore, in a subgroup of participants assessed by the tridimensional personality questionnaire, novelty seeking is correlated with the extent of left lateralization of AI connectivity to the pallidum and putamen in men and with the extent of right lateralization of AI connectivity to the parahippocampal gyrus in women. These findings support hemispheric functional differentiation of the AI.