Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of undernutrition in foetal life on energy expenditure during gestation in ewes

The long-term effect of early life undernutrition on late gestation energy expenditure (EEgest) was investigated in sheep. Ewes were fed either adequate (100%) or restricted (60%) energy and protein during late foetal life as well as during last trimester of gestation later in life, resulting in three groups: Adequate-Adequate (AA, n = 5), Adequate-Restricted (AR, n = 5) and Restricted-Restricted (RR, n = 5). At two weeks pre-partum, EEgest were calculated from respiratory gaseous exchange and nitrogen excreted in urine and further it was partitioned to energy expenditure for conceptus development (EEconceptus) and homeorhetic adaptations in maternal metabolism (EEhomeorhetic). Late gestational energy and protein restriction reduced the EEgest in the AR ewes (4.1 MJ · d−1) but not in the RR ewes (5.2 MJ · d−1) compared with the AA ewes (6.8 MJ · d−1). Based on conceptus-weight, no significant difference was found in EEhomeorhetic among the groups; 172, 175 and 169 kJ/kg · d−1 in AA, AR and RR ewes, respectively. However, EEconceptus was significantly lower in AR (135 kJ/kg · d−1) in comparison with AA (298 kJ/kg · d−1) and RR (252 kJ/kg · d−1) ewes. In conclusion, exposure nutrient restriction in early life impairs the ability of ewes to respond to nutritional restriction in terms of energy expenditure of gestation.
Digital margins: Social and digital exclusion of Gypsy-Travelers in the Netherlands

Research on digital inclusion increasingly focuses on vulnerable groups, with the prevailing idea that social exclusion leads to digital exclusion. The role of the socio-spatial context is often faded into the background due to user-centric (individual) approaches. This article explores how a vulnerable group, Gypsy-Travelers in the Netherlands, deals with digital developments within their socio-spatial context. Contrary to prevailing theories, the analysis shows that Gypsy-Travelers are digitally engaged, despite their social exclusion. An advantage of the Gypsy-Traveler culture is that extended families on the sites provide a large potential of proxy users for support. Many of the Gypsy-Travelers are digitally engaged, but they engage and participate on their own terms. Furthermore, the digital engagement of Gypsy-Travelers is not a panacea for their social exclusion. In fact, their problematic relation with the settled society is mirrored in online activities. This research shows that digitalization has added a new layer to the interaction between Gypsy-Travelers and settled society. It also demonstrates that more socially and spatially contextualized research approaches can add insights to the debate on social and digital exclusion.
Genomic Polymorphism of the Pandemic A (H1N1) Influenza Viruses Correlates with Viral Replication, Virulence, and Pathogenicity In Vitro and In Vivo

The novel pandemic A (H1N1) virus was first identified in Mexico in April 2009 and quickly spread worldwide. Like all influenzas, the H1N1 strain-specific properties of replication, virulence, and pathogenicity are a result of the particular genomic sequence and concerted expression of multiple genes. Thus, specific mutations may support increased virulence and may be useful as biomarkers of potential threat to human health. We performed comparative genomic analysis of ten strains of the 2009 pandemic A (H1N1) influenza viruses to determine whether genotypes associated with clinical phenotypes, which ranged from mild to severe illness and up to lethal. Virus replication capacity was tested for each strain in vitro using cultured epithelial cells, while virulence and pathogenicity were investigated in vivo using the BALB/c mouse model. The results indicated that A/Sichuan/1/2009 strain had significantly higher replication ability and virulence than the other strains, and five unique non-synonymous mutations were identified in important gene-encoding sequences. These mutations led to amino acid substitutions in HA (L32I), PA (A343T), PB1 (K353R and T566A), and PB2 (T471M), and may be critical molecular determinants for replication, virulence, and pathogenicity. Our results suggested that the replication capacity in vitro and virulence in vivo of the 2009 pandemic A (H1N1) viruses were not associated with the clinical phenotypes. This study offers new insights into the transmission and evolution of the 2009 pandemic A (H1N1) virus.
Winter wheat morphology response to cold temperature stress during autumn acclimation

Winter wheat (Triticum aestivum L.) abilities depend on development during autumn acclimation. The plant ability of acclimation to low temperatures is closely associated with the photosynthesis level, leaf area index (LAI), root system development. This study investigated the effect of liquid humic fertilizers (LHF) on biometric characteristics, namely LAI, root and shoot development. The fertilizers were applied in conventional and organic growth technologies of w. wheat to adapt to the low temperatures during autumn acclimation. Winter wheat «Širvinta 1» was grown in different rotation fields of conventional (CF; Albi-EpihypogleyicLuvisol, LVg-p-w-ab) and organic (OF; Hapli-EpihypogleyicLuvisol, LVg-p-w-ha) farming of Training Farm at Aleksandras Stulginskis University (ASU) during 2010–2011. The obtained results confirmed the significant LHF influence on enhancing winter wheat biometrical indices and seedling growth. Nonetheless, seed felting exhibited stronger effect on LAI (increased by 0.7-1.1 g m-1 day-1 in OF and 0.25-0.7 g m-1 day-1 in CF), root length (increased by 1166 mm in OF and 1182.55 mm in CF) and area (increased by 72.45 mm2 in OF and 588.7 mm2 in CF) during autumn acclimation rather than seedling spraying.
Indices of anti‐dengue immunoglobulin G subclasses in adult Mexican patients with febrile and hemorrhagic dengue in the acute phase

Heterologous secondary infections are at increased risk of developing dengue hemorrhagic fever (DHF) because of antibody‐dependent enhancement (ADE). IgG subclasses can fix and activate complement and bind to Fcɣ receptors. These factors may also play an important role in the development of ADE and thus in the pathogenesis of DHF. The aim of this study was to analyze the indices of anti‐dengue IgG subclasses in adult patients with febrile and hemorrhagic dengue in the acute phase. In 2013, 129 patients with dengue fever (DF) and 57 with DHF in Veracruz, Mexico were recruited for this study and anti‐dengue IgM and IgG determined by capture ELISA. Anti‐dengue IgG subclasses were detected by indirect ELISA. Anti‐dengue IgG2 and IgG3 subclasses were detected in patients with dengue. IgG1 increased significantly in the sera of patients with both primary and secondary infections and DHF, but was higher in patients with secondary infections. The IgG4 subclass index was significantly higher in the sera of patients with DHF than in that of those with DF, who were in the early and late acute phase of both primary and secondary infection. In conclusion, indices of subclasses IgG1 and IgG4 were higher in patients with DHF.
Effects of distributed practice on the proceduralization of morphology

The present study aimed to examine whether distributed practice works better than massed practice for proceduralization of grammatical knowledge. Learners of Japanese as a second language were trained on an element of Japanese morphology under either massed or distributed practice conditions. Results showed that massed practice led to accurate utterances to the same extent as distributed practice. It was also shown that massed practice may lead to more rapid utterances than distributed practice. A number of potential factors that mediate the effects of distributed practice are discussed.
Effect of growth rate and cell shape on the peptidoglycan composition in Escherichia coli

The muropeptide composition of peptidoglycan from Escherichia coli W7 cultivated at different growth rates in chemostat cultures was compared by using high-pressure liquid chromatography. At a low growth rate (D = 0.1 h-1), about 40% more covalently bound lipoprotein and at least twofold more diaminopimelyl-diaminopimelic acid cross-bridges were found than at a high growth rate (D = 0.8 h-1). The total degree of cross-linkage was only slightly increased, and the fraction of trimeric muropeptides and the average length of the glycan chains were not changed significantly. Analysis of the peptidoglycan from a morphological variant strain of W7 revealed that the altered peptidoglycan composition in slowly growing W7 cells was not correlated with the observation that these cells, due to their decreased cell length, were relatively enriched in polar material. In fact, our results suggested that peptidoglycan forming cell poles is chemically identical to that forming lateral wall.
UNDERSTANDING THE DIVERGENT INFLUENCES OF READING ACTIVITIES ON THE COMPREHENSION OF SHORT STORIES

This study aims at understanding how the use of different reading activities affects readers’ comprehension of short stories. Forty-seven students with an advanced level of English proficiency participated in the study where a quasi-experimental research design was pursued. The experimental and control groups of students completed different sets of activities on the same short story. The experimental group was given a set of activities comprising previewing, predicting, keywords, scanning, skimming, clarifying, summarising, question and answer, and drawing conclusions; while the control group did activities including brainstorming, predicting, surveying, reciprocal teaching, evaluating, inferring, rereading, thinking aloud, discussion, and summarising activities. A post-test measured both literal comprehension and evaluation of the textual information. Statistical analysis revealed that the experimental group outperformed the control group on literal comprehension while the control group did better on evaluation questions, implying a differential influence of the activities on different types of comprehension. The study suggests that reading teachers need to be sensitive to the requirements of comprehension tasks in their selection of reading activities.
Improving Communication-specific Coping after Traumatic Brain Injury: Evaluation of a New Treatment using Single-case Experimental Design

Background and aims: Impaired communication is a well-documented and enduring consequence of traumatic brain injury (TBI). As a result of this impairment, people with TBI frequently experience communication breakdown and associated stress. Typically, we use communication-specific coping strategies in situations characterised by communication breakdown. Productive strategies enhance message transfer; non-productive strategies do little to resolve problems and frequently result in negative social interaction. This research aimed to evaluate the effectiveness of a new treatment, Communication-specific Coping Intervention (CommCope-I), which specifically targets coping in the context of communication breakdown. Method: Single-case experimental design (A–B–A with follow-up using multiple probes) across two participants was used. Participants were Samantha, a 30-year-old woman who had sustained severe TBI 8 years previously, and Thomas, a 34-year-old man who had sustained severe TBI when he was 29 years old. CommCope-I is a 6-week programme which targets personally relevant productive coping strategies identified collaboratively with the client. Productive coping scripts are developed and practised through a series of graded scenarios that are evaluated with the aid of video recording. Results: Percentage of non-overlapping corrected data (PNCD) was used to analyse the results. PNCD involves a data-correction procedure to remove baseline trend from the data series prior to calculating the change produced as a result of intervention. A large treatment effect was demonstrated in both participants (PNCD: end of treatment Samantha = 100%, Thomas = 100%, 3-month follow-up Samantha = 100%, Thomas = 100%). These results are consistent with highly effective treatment. Conclusions: This study provides sound phase-1 evidence for the effectiveness of CommCope-I.
Characterization of Radially Symmetric Finite Time Blowup in Multidimensional Aggregation Equations

This paper studies the transport of a mass $\mu$ in $\mathbb{R}^d, d \geq 2,$ by a flow field $v= -\nabla K*\mu$. We focus on kernels $K=|x|^\alpha/ \alpha$ for $2-d\leq \alpha 2$ where radially symmetric solutions are known to lose monotonicity. In the case of the Newtonian potential ($\alpha=2-d$), under the assumption of radial symmetry the equation can be transformed into the inviscid Burgers equation on a half line. This enables us to prove preservation of monoto.
Design pattern directed clustering for understanding open source code

Program understanding plays an important role in the maintenance and reuse of open source code. Rapid evolving and bad documentation makes the understanding and reusing difficult. Design patterns are widely employed in the open source code. In this paper, we propose a design pattern directed clustering approach to help understand the structure of open source code. According to the approach, we have implemented a prototype tool. We also conducted an experiment on an open source system to evaluate it.
Involvement of hepatocyte growth factor in formation of bronchoalveolar structures in embryonic rat lung in primary culture.

To clarify the role of hepatocyte growth factor (HGF) in embryonic lung development, organoids from fetal rat lung were cultured in collagen gels with or without HGF antisense oligonucleotides. Cyst-like structures formed within 24 h in organoids isolated from fetuses after 14 days' gestation, but this was abolished by the oligonucleotide addition, apparently by interference with the endogenous expression of HGF. Electron microscopy revealed two types of structure: an alveolar type characterized by osmiophilic lamellar bodies in the cytoplasm and lumen, and a bronchial type consisting of epithelial cells bearing microvilli on their apical surfaces. HGF mRNA was detectable from day 14 in fetal lung by RT-PCR. Our results suggest that HGF plays, coordinately with its expression, a crucial role in the morphogenesis of both alveolar and bronchial epithelia in the rat fetal lung.
Gremlin is Overexpressed in Lung Adenocarcinoma and Increases Cell Growth and Proliferation in Normal Lung Cells

Background Gremlin, a member of the Dan family of BMP antagonists, is a glycosylated extracellular protein. Previously Gremlin has been shown to play a role in dorsal-ventral patterning, in tissue remodeling, and recently in angiogenesis. Evidence has previously been presented showing both over- and under-expression of Gremlin in different tumor tissues. Here, we sought to quantify expression of Gremlin in cancers of the lung and performed in vitro experiments to check whether Gremlin promotes cell growth and proliferation. Methodology/Principal Findings Expression of Gremlin in 161 matched tumor and normal lung cancer specimens is quantified by quantitative real-time PCR and protein level is measured by immunohistochemistry. GREM1 was transfected into lung fibroblast and epithelial cell lines to assess the impact of overexpression of Gremlin in vitro. Results Lung adenocarcinoma but not squamous cell carcinoma shows a significant increase in Gremlin expression by mRNA and protein level. Lung fibroblast and epithelial cell lines transfected with GREM1 show significantly increased cell proliferation. Conclusions/Significance Our data suggest that Gremlin acts in an oncogenic manner in lung adenocarcinoma and could hold promise as a new diagnostic marker or potential therapeutic target in lung AD or general thoracic malignancies.
Cdc6 contributes to cisplatin-resistance by activation of ATR-Chk1 pathway in bladder cancer cells

High activation of DNA damage response is implicated in cisplatin (CDDP) resistance which presents as a serious obstacle for bladder cancer treatment. Cdc6 plays an important role in the malignant progression of tumor. Here, we reported that Cdc6 expression is up-regulated in bladder cancer tissues and is positively correlated to high tumor grade. Cdc6 depletion can attenuate the malignant properties of bladder cancer cells, including DNA replication, migration and invasion. Furthermore, higher levels of chromatin-binding Cdc6 and ATR were detected in CDDP-resistant bladder cancer cells than in the parent bladder cancer cells. Intriguingly, down-regulation of Cdc6 can enhance sensitivity to CDDP both in bladder cancer cells and CDDP-resistant bladder cancer cells. Cdc6 depletion abrogates S phase arrest caused by CDDP, leading to aberrant mitosis by inactivating ATR-Chk1-Cdc25C pathway. Our results indicate that Cdc6 may be a promising target for overcoming CDDP resistance in bladder cancer.
Characterization of basal and lipopolysaccharide-induced microRNA expression in equine peripheral blood mononuclear cells using Next-Generation Sequencing

The innate immune response to lipopolysaccharide contributes substantially to the morbidity and mortality of gram-negative sepsis. Horses and humans share an exquisite sensitivity to lipopolysaccharide and thus the horse may provide valuable comparative insights into this aspect of the inflammatory response. MicroRNAs, small non-coding RNA molecules acting as post-transcriptional regulators of gene expression, have key roles in toll-like receptor signaling regulation but have not been studied in this context in horses. The central hypothesis of this study was that lipopolysaccharide induces differential microRNA expression in equine peripheral blood mononuclear cells in a manner comparable to humans. Illumina Next Generation Sequencing was used to characterize the basal microRNA transcriptome in isolated peripheral blood mononuclear cells from healthy adult horses, and to evaluate LPS-induced changes in microRNA expression in cells cultured for up to four hours. Selected expression changes were validated using quantitative reverse-transcriptase PCR. Only miR-155 was significantly upregulated by LPS, changing in parallel with supernatant tumor necrosis factor-α concentration. Eight additional microRNAs, including miR-146a and miR-146b, showed significant expression change with time in culture without a clear LPS effect. Target predictions indicated a number of potential immunity-associated targets for miR-155 in the horse, including SOCS1, TAB2 and elements of the PI3K signaling pathway, suggesting that it is likely to influence the acute inflammatory response to LPS. Gene alignment showed extensive conservation of the miR-155 precursor gene and associated promoter regions between horses and humans. The basal and LPS-stimulated microRNA expression pattern characterized here were similar to those described in human leukocytes. As well as providing a resource for further research into the roles of microRNAs in immune responses in horses, this will facilitate inter-species comparative study of the role of microRNAs in the inflammatory cascade during endotoxemia and sepsis.
Listeria monocytogenes σB Modulates PrfA-Mediated Virulence Factor Expression

ABSTRACT Listeria monocytogenes σB and positive regulatory factor A (PrfA) are pleiotropic transcriptional regulators that coregulate a subset of virulence genes. A positive regulatory role for σB in prfA transcription has been well established; therefore, observations of increased virulence gene expression and hemolytic activity in a ΔsigB strain initially appeared paradoxical. To test the hypothesis that L. monocytogenes σB contributes to a regulatory network critical for appropriate repression as well as induction of virulence gene expression, genome-wide transcript profiling and follow-up quantitative reverse transcriptase PCR (qRT-PCR), reporter fusion, and phenotypic experiments were conducted using L. monocytogenes prfA*, prfA* ΔsigB, ΔprfA, and ΔprfA ΔsigB strains. Genome-wide transcript profiling and qRT-PCR showed that in the presence of active PrfA (PrfA*), σB is responsible for reduced expression of the PrfA regulon. σB-dependent modulation of PrfA regulon expression reduced the cytotoxic effects of a PrfA* strain in HepG2 cells, highlighting the functional importance of regulatory interactions between PrfA and σB. The emerging model of the role of σB in regulating overall PrfA activity includes a switch from transcriptional activation at the P2prfA promoter (e.g., in extracellular bacteria when PrfA activity is low) to posttranscriptional downregulation of PrfA regulon expression (e.g., in intracellular bacteria when PrfA activity is high).
Length-dependent tension in the failing heart and the efficacy of cardiac resynchronization therapy.

AIMS Cardiac resynchronization therapy (CRT) has emerged as one of the few effective and safe treatments for heart failure. However, identifying patients that will benefit from CRT remains controversial. The dependence of CRT efficacy on organ and cellular scale mechanisms was investigated in a patient-specific computer model to identify novel patient selection criteria. METHODS AND RESULTS A biophysically based patient-specific coupled electromechanics heart model has been developed which links the cellular and sub-cellular mechanisms which regulate cardiac function to the whole organ function observed clinically before and after CRT. A sensitivity analysis of the model identified lack of length dependence of tension regulation within the sarcomere as a significant contributor to the efficacy of CRT. Further simulation analysis demonstrated that in the whole heart, length-dependent tension development is key not only for the beat-to-beat regulation of stroke volume (Frank-Starling mechanism), but also the homogenization of tension development and strain. CONCLUSIONS In individuals with effective Frank-Starling mechanism, the length dependence of tension facilitates the homogenization of stress and strain. This can result in synchronous contraction despite asynchronous electrical activation. In these individuals, synchronizing electrical activation through CRT may have minimal benefit.
Parkin overexpression selects against a deleterious mtDNA mutation in heteroplasmic cybrid cells

Mitochondrial genomes with deleterious mutations can replicate in cells along with wild-type genomes in a state of heteroplasmy, and are a cause of severe inherited syndromes, such as mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke (MELAS), neuropathy, ataxia, retinitis pigmentosa-maternally inherited Leigh syndrome (NARP-MILS), and Leber's hereditary optic neuropathy (LHON). The cytosolic E3 ligase, Parkin, commonly mutated in recessive familial parkinsonism, translocates to depolarized mitochondria and induces their autophagic elimination, suggesting that Parkin may signal the selective removal of defective mitochondria within the cell. We report that long-term overexpression of Parkin can eliminate mitochondria with deleterious COXI mutations in heteroplasmic cybrid cells, thereby enriching cells for wild-type mtDNA and restoring cytochrome c oxidase activity. After relieving cybrid cells of Parkin overexpression, a more favorable wild-type to mutant mitochondrial genome ratio is stably maintained. These data support the model that Parkin functions in a mitochondrial quality control pathway. Additionally, they suggest that transiently increasing levels of Parkin expression might ameliorate certain mitochondrial diseases.