Miracle-dz/UniFAR-FTUs huggingface dataset:
On the effectiveness of mutation analysis as a black box testing technique

The technique of mutation testing, in which the effectiveness of tests is determined by creating variants of a program in which statements are mutated, is well known. Whilst of considerable theoretical interest, the technique requires costly tools and is computationally expensive. Very large numbers of 'mutants' can be generated for even simple programs. More recently, it has been proposed that the concept be applied to specification based (black box) testing. The proposal is to generate test cases by systematically replacing data items relevant to a particular part of a specification with a data item relevant to another. If the specification is considered as generating a language that describes the set of valid inputs, then the mutation process is intended to generate syntactically valid and invalid statements. Irrespective of their 'correctness' in terms of the specification, these can then be used to test a program in the usual (black box) manner. For this approach to have practical value it must produce test cases that would not be generated by other popular black box test generation approaches. The paper reports a case study involving the application of mutation based black box testing to two programs of different types. Test cases were also generated using equivalence class testing. and boundary value testing approaches. The test cases from each method were examined to judge the overlap and to assess the value of the additional cases generated. It was found that less than 20% of the mutation test cases for a data-vetting program were generated by the other two methods, as against 75% for a statistical analysis program. The paper analyses these results and suggests classes of specifications for which mutation based test-case generation may be effective.
Safety of Epicenter Versus Intact Parenchyma as a Transplantation Site for Human Neural Stem Cells for Spinal Cord Injury Therapy

Neural stem cell transplantation may have the potential to yield repair and recovery of function in central nervous system injury and disease, including spinal cord injury (SCI). Multiple pathological processes are initiated at the epicenter of a traumatic spinal cord injury; these are generally thought to make the epicenter a particularly hostile microenvironment. Conversely, the injury epicenter is an appealing potential site of therapeutic human central nervous system‐derived neural stem cell (hCNS‐SCns) transplantation because of both its surgical accessibility and the avoidance of spared spinal cord tissue. In this study, we compared hCNS‐SCns transplantation into the SCI epicenter (EPI) versus intact rostral/caudal (R/C) parenchyma in contusion‐injured athymic nude rats, and assessed the cell survival, differentiation, and migration. Regardless of transplantation site, hCNS‐SCns survived and proliferated; however, the total number of hCNS‐SCns quantified in the R/C transplant animals was twice that in the EPI animals, demonstrating increased overall engraftment. Migration and fate profile were unaffected by transplantation site. However, although transplantation site did not alter the proportion of human astrocytes, EPI transplantation shifted the localization of these cells and exhibited a correlation with calcitonin gene‐related peptide fiber sprouting. Critically, no changes in mechanical allodynia or thermal hyperalgesia were observed. Taken together, these data suggest that the intact parenchyma may be a more favorable transplantation site than the injury epicenter in the subacute period post‐SCI.
Significance of Notch1-signaling Pathway in Human Pancreatic Development and Carcinogenesis

In animal studies, Notch1-signaling pathway plays an important role in the pancreatic embryogenesis by promoting pancreatic progenitor cells self-renewal and exocrine linage development. The persistent activation of Notch pathway could arrest the organ development and keep cells at an undifferentiated stage. Studies have shown that Notch1-signaling pathway is upregulated in invasive pancreatic ductal adenocarcinoma (PDAC). Here we examined the expression pattern of Notch1 and Hes1 in human fetal pancreatic tissues to elucidate the role of Notch1 in human pancreatic embryonic development. We also compared Notch1 expression in tissues from PDAC, chronic pancreatitis and pancreatic intraepithelial neoplasm. Our data show that Notch1/Hes1-signaling pathway is activated during early pancreatic embryogenesis and reaches the highest at birth. After pancreas is fully developed, Notch1/Hes1 pathway is inactivated even though Notch1 protein cell-surface expression is upregulated. We also showed that the expression of both Notch1 and Hes1 are present in 50% (33/66) of PDACs, but not in pancreatic intraepithelial neoplasms. These findings indicate that Notch1 activation is only apparent in late stage of pancreatic carcinogenesis, suggesting that treatment with Notch-signaling inhibitors including &ggr;-secretase should be selectively used for PDACs with confirmed Notch1-signaling activation.
A three-dimensional finite element model from computed tomography data: A semi-automated method

Abstract Three-dimensional finite element analysis is one of the best ways to assess stress and strain distributions in complex bone structures. However, accuracy in the results may be achieved only when accurate input information is given. A semi-automated method to generate a finite element (FE) model using data retrieved from computed tomography (CT) was developed. Due to its complex and irregular shape, the glenoid part of a left embalmed scapula bone was chosen as working material. CT data were retrieved using a standard clinical CT scanner (Siemens Somatom Plus 2, Siemens AG, Germany). This was done to produce a method that could later be utilized to generate a patient-specific FE model. Different methods of converting Hounsfield unit (HU) values to apparent densities and subsequently to Young's moduli were tested. All the models obtained were loaded using three-dimensional loading conditions taken from literature, corresponding to an arm abduction of 90°. Additional models with different amounts of elements were generated to verify convergence. Direct comparison between the models showed that the best method to convert HU values directly to apparent densities was to use different equations for cancellous and cortical bone. In this study, a reliable method of determining both geometrical data and bone properties from patient CT scans for the semi-automated generation of an FE model is presented.
Population Structure, Genetic Diversity, Effective Population Size, Demographic History and Regional Connectivity Patterns of the Endangered Dusky Grouper, Epinephelus marginatus (Teleostei: Serranidae), within Malta’s Fisheries Management Zone

The objective of this study is to describe the genetic population structure and demographic history of the endangered marine fish, Epinephelus marginatus, within Malta’s Fisheries Management Zone for the purpose of localised conservation planning. Epinephelus marginatus is a long-lived, sedentary, reef-associated protogynous hermaphrodite with high commercial and recreational value that is at risk of extinction throughout its global distribution. Based on global trends, population substructuring and gaps in local knowledge this has led to an increased interest in evaluation of local stock. Assessment of Maltese demography was based on historical and contemporary catch landings data whilst genetic population structure and regional connectivity patterns were evaluated by examining 175 individuals collected within the central Mediterranean region between 2002 and 2009 using 14 nuclear microsatellite loci. Demographic stock assessment of Maltese E. marginatus’ revealed a 99% decline in catch landings between 1947 and 2009 within the Fisheries Management Zone. A contemporary modest mean size was observed, 3 ± 3 kg, where approximately 17% of the population was juvenile, 68% female/sex-changing and 15% were male with a male-to-female sex ratio of 1:5. Genetic analysis describes the overall population of E. marginatus’ within the Fisheries Management Zone as decreasing in size (ƟH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, p < 0.001) with an estimated effective population size of 130 individuals. Results of spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within Malta’s Fisheries Management Zone and that they are connected to a larger network of E. marginatus’ within the Sicily Channel. Results suggest conservation management should be designed to reflect E. marginatus’ within Malta’s Fisheries Management Zone as two management units.
Severity of White Matter Hyperintensities and Length of Hospital Stay in Patients with Cognitive Impairment: A CREDOS (Clinical Research Center for Dementia of South Korea) Study.

BACKGROUND & OBJECTIVE White matter hyperintensities (WMHs) contribute to aggravation of dementia or geriatric syndrome, thereby resulting in functional impairment. However, evidence of direct association between WMHs and medical resource utilization indicated by length of hospital stay (LOS) is scarce in patients with cognitive impairment. This study aimed to examine the relationship between the severity of WMHs and LOS in patients with cognitive impairment. METHODS 4,253 older adults with cognitive impairment were enrolled in this study. We defined LOS as the total sum of days from January 1, 2008 to December 31, 2012. The severity of periventricular (PVWMHs), deep (DWMHs), and overall white matter hyperintensities (Overall WMHs) was evaluated by a visual rating scale. We conducted multinomial logistic regression to demonstrate the relationship between LOS and severity of PVWHMs, DWHMs, and Overall WMHs, respectively. RESULTS The median LOS was 20 days. Severe PVWMHs had a higher likelihood of longer LOS (Q3: odd ratio/OR = 1.32, 95% confidence interval/CI = 1.06-1.64; Q4: OR = 1.33, 95% CI = 1.07-1.65; Q5: OR = 1.55, 95% CI = 1.26-1.91). As for DWMHs, moderate DWMHs were related to longer LOS (Q4: OR = 1.33, 95% CI = 1.03-1.71; Q5: OR = 1.63, 95% CI = 1.26-2.11). Finally, severity of overall WMHs was independently associated with LOS, which was similar to the results of DWMHs. CONCLUSION These findings would advocate for prevention of WMHs to stave off excess medical resource utilization in patients with cognitive impairment.
Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity

Significance Vibrio cholerae biofilms are hyperinfectious, yet the mechanisms underpinning this phenomenon remain poorly understood. We analyzed V. cholerae intestinal infection in three-dimensional space, using imaging and quantification tools and uncovered differences in the biogeography of the small intestine infected with biofilm-grown cells compared to planktonic-grown cells. Our experiments show that V. cholerae biofilm-grown cells upregulate virulence factors compared to planktonic-grown cells, priming biofilm-grown cells for infection and driving a hyperinfectious biofilm phenotype. Collectively, this work establishes a method for studying V. cholerae infection and enhances our understanding of V. cholerae virulence mechanisms and the importance of biofilms in contributing to acute infections. Vibrio cholerae remains a major global health threat, disproportionately impacting parts of the world without adequate infrastructure and sanitation resources. In aquatic environments, V. cholerae exists both as planktonic cells and as biofilms, which are held together by an extracellular matrix. V. cholerae biofilms have been shown to be hyperinfective, but the mechanism of hyperinfectivity is unclear. Here we show that biofilm-grown cells, irrespective of the surfaces on which they are formed, are able to markedly outcompete planktonic-grown cells in the infant mouse. Using an imaging technique designed to render intestinal tissue optically transparent and preserve the spatial integrity of infected intestines, we reveal and compare three-dimensional V. cholerae colonization patterns of planktonic-grown and biofilm-grown cells. Quantitative image analyses show that V. cholerae colonizes mainly the medial portion of the small intestine and that both the abundance and localization patterns of biofilm-grown cells differ from that of planktonic-grown cells. In vitro biofilm-grown cells activate expression of the virulence cascade, including the toxin coregulated pilus (TCP), and are able to acquire the cholera toxin-carrying CTXФ phage. Overall, virulence factor gene expression is also higher in vivo when infected with biofilm-grown cells, and modulation of their regulation is sufficient to cause the biofilm hyperinfectivity phenotype. Together, these results indicate that the altered biogeography of biofilm-grown cells and their enhanced production of virulence factors in the intestine underpin the biofilm hyperinfectivity phenotype.
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater

Background Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. Methods On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community. Results Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems. Conclusions The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds.
Life Satisfaction In Adults With Pediatric-Onset Spinal Cord Injuries

Abstract Objective: To determine the level of life satisfaction of adults with pediatric-onset spinal cord injuries (SCI) and the factors associated with life satisfaction. Method: A structured interview including standardized measures. Participants: Participants were individuals who sustained SCI at age 18 years or younger, were 24 years of age or older at interview, did not have significant brain injury, and were living in the United States or Canada. Outcome measures: A structured interview, the Functional Independence Measure (FIM), the Craig Handicap Assessment and Reporting Technique (CHART), the Short-Form 12 (SF-12), and the Satisfaction with Life Scale (SWLS). Results: Two hundred sixteen individuals were interviewed. Mean age at injury was 14 years, mean age at interview was 29 years, and mean duration of injury was 14 years. The mean SWLS score was 23.6, and the median score was 25. There was not a significant difference between men and women, but those with tetraplegia were significantly less satisfied than were those with paraplegia. A regression model identified age at injury, community mobility (CHART), marital status, use of street drugs, perceived mental health (SF-12), and medical complications as predictors of life satisfaction. Other factors strongly associated with SWLS were employment, income, independent living, FIM total plus physical and sociocognitive domain scores, perceived physical health (SF-12), and CHART total plus the subscales of physical independence, cognitive independence, and occupation. Conclusions: Life satisfaction in adults with pediatric-onset SCI is associated with demographic, injury-related, and functional limitation factors, as well as with health status and community integration outcomes.
Link Budget and Capacity Performance of Inductively Coupled Resonant Loops

A near field power transfer equation for an inductively coupled near field system, analogous to Friis transmission equation for far field communications, is derived based on the equivalent circuit model of the coupled resonant loops. Experimental results show the proposed near field coupling equation is trustworthy as it correctly predicts the transferred power versus distance relationship for different values of loaded quality factors at the transmitter and the receiver. Capacity performance of near field communication (NFC) links are analyzed based on information theory, respectively for noise limited and interference limited scenarios. The analytical results provide guidelines for power and capacity budget in inductively coupled antenna systems. Examples of inductively coupled VLF NFC links are evaluated for different operating scenarios, demonstrating the efficacy and importance of the proposed method for near field link budget.
Analysis of Imprinted Messenger RNA Expression During Bovine Preimplantation Development1

Abstract While the expression and epigenetic differences of imprinted genes have been extensively characterized in the mouse and human, little is known about imprinted genes in livestock species. In the current study, eight genes that are imprinted in the human or mouse were investigated in preimplantation bovine embryos. Amplified cDNA was created from three single metaphase II (MII) oocytes or embryos throughout preimplantation development. The imprinted genes Dlk1 and Mest (isoform 1) had no detectable transcripts during preimplantation development. Gnas and Grb10 were expressed in most embryos from the 2-cell to blastocyst stages of development. Mest (isoform 2) was expressed in all oocytes and embryos, except for one blastocyst sample. Ndn and Xist were expressed from the 8–16-cell stage (maternal-to-zygotic transition, MZT) onwards. Sgce was expressed until the MZT, and Nnat in both early (α form) and late (β form) stage embryos. The paternally imprinted genes Gnas, Grb10, and Xist were expressed in both in vitro-fertilized (IVF) and parthenogenetically activated (PA) blastocysts as expected. Of the four maternally imprinted genes expressed in the blastocyst (Mest, Ndn, Nnat, and Sgce), Nnat alone showed differential mRNA expression between IVF and PA blastocysts, suggesting imprinting by this stage of development. In conclusion, seven of the eight genes investigated showed mRNA expression during preimplantation development, indicating a potential role during early development. Also significant is the observation that Nnat is imprinted by the blastocyst stage of development although the other genes are not, indicating a temporal imprinting program.
Synergism between Calcium and Cyclic GMP in Cyclic AMP Response Element-Dependent Transcriptional Regulation Requires Cooperation between CREB and C/EBP-β

ABSTRACT Calcium induces transcriptional activation of the fos promoter by activation of the cyclic AMP response element (CRE)-binding protein (CREB), and in some cells its effect is enhanced synergistically by cyclic GMP (cGMP) through an unknown mechanism. We observed calcium-cGMP synergism in neuronal and osteogenic cells which express type II cGMP-dependent protein kinase (G-kinase); the effect on the fos promoter was mediated by the CRE and proportional to G-kinase activity. Dominant negative transcription factors showed involvement of CREB- and C/EBP-related proteins but not of AP-1. Expression of C/EBP-β but not C/EBP-α or -δ enhanced the effects of calcium and cGMP on a CRE-dependent reporter gene. The transactivation potential of full-length CREB fused to the DNA-binding domain of Gal4 was increased synergistically by calcium and cGMP, and overexpression of C/EBP-β enhanced the effect, while a dominant negative C/EBP inhibited it. With a mammalian two-hybrid system, coimmunoprecipitation experiments, and in vitro binding studies, we demonstrated that C/EBP-β and CREB interacted directly; this interaction involved the C terminus of C/EBP-β but occurred independently of CREB's leucine zipper domain. CREB Ser133 phosphorylation was stimulated by calcium but not by cGMP; in cGMP-treated cells, 32PO4 incorporation into C/EBP-β was decreased and C/EBP-β/CRE complexes were increased, suggesting regulation of C/EBP-β functions by G-kinase-dependent dephosphorylation. C/EBP-β and CREB associated with the fos promoter in intact cells, and the amount of promoter-associated C/EBP-β was increased by calcium and cGMP. We conclude that calcium and cGMP transcriptional synergism requires cooperation of CREB and C/EBP-β, with calcium and cGMP modulating the phosphorylation states of CREB and C/EBP-β, respectively.
High-calcium mineral water as a calcium supplementing measure for post-thyroidectomy hypocalcemia.

AIM The aim of this study was to test the possibility of enhancing blood calcium levels in totally thyroidectomized patients by supplementation with 1 L/d carbonate-bicarbonate-high-calcium mineral water. METHODS This study enrolled 95 outpatients, totally thyroidectomized four months earlier, and hence treated with oral calcium and vitamin-D. At recruitment, ionized blood calcium was either below (Group A; N. 55) or above (Group B; N. 40, randomly divided in Group B1 [N. 20] and Group B2 [N.20]) the lower limit of the normal range (1.12 mmol/L). For one month, Group A was treated with 1 L/d high-calcium (483 mg/L) mineral water and continued the usual therapy with Ca and vitamin-D. In contrast, Group B1 and Group B2 substituted their Ca and vitamin-D therapy with 1 L/d high-calcium mineral water (Group B1) or 1 L/d of placebo mineral water (Ca:80 mg/L) (Group B2). RESULTS After one month, a significant 7.5% increase in blood ionized-calcium levels was observed in Group A, no change in Group B1 and a significant drop below normality in Group B2 (Group B2 vs Group B1, P<0.001). Thereafter, 1 L/d of the high-calcium mineral water, given to Group B2 instead of placebo for an additional month, significantly enhanced ionized-calcium levels above the lower limit of normality (Group B2 vs Group B1, NS). CONCLUSION These experiments show that calcium supplementation as 1 L/d of a high-calcium mineral water may efficaciously enhance blood calcium levels in thyroidectomized patients. This complementary treatment might at least in part contribute to the prevention and/or treatment of hypocalcemia and substitute vitamin-D and calcium therapies after thyroidectomy.