Miracle-dz/UniFAR-FTUs huggingface dataset:
How microbial ancient DNA, found in association with human remains, can be interpreted.

The analysis of the DNA of ancient micro-organisms in archaeological and palaeontological human remains can contribute to the understanding of issues as different as the spreading of a new disease, a mummification process or the effect of diets on historical human populations. The quest for this type of DNA, however, can represent a particularly demanding task. This is mainly due to the abundance and diffusion of bacteria, fungi, yeasts, algae and protozoans in the most diverse environments of the present-day biosphere and the resulting difficulty in distinguishing between ancient and modern DNA. Nevertheless, at least under some special circumstances, by using rigorous protocols, which include an archaeometric survey of the specimens and evaluation of the palaeoecological consistency of the results of DNA sequence analysis, glimpses of the composition of the original microbial flora (e.g. colonic flora) can be caught in ancient human remains. Potentials and pitfalls of this research field are illustrated by the results of research works performed on prehistoric, pre-Columbian and Renaissance human mummies.
HMGB1 Interacts with Many Apparently Unrelated Proteins by Recognizing Short Amino Acid Sequences*

The chromatin high mobility group protein 1 (HMGB1) is a very abundant and conserved protein that is structured into two HMG box domains plus a highly acidic C-terminal domain. From the ability to bind DNA nonspecifically and to interact with various proteins, several functions in DNA-related processes have been assigned to HMGB1. Nevertheless, its functional role remains the subject of controversy. Using a phage display approach we have shown that HMGB1 can recognize several peptide motifs. A computer search of the protein data bases found peptide homologies with proteins already known to interact with HMGB1, like p53, and have allowed us to identify new potential candidates. Among them, transcriptional activators like the heterogeneous nuclear ribonucleoprotein K (hnRNP K), repressors like methyl-CpG binding protein 2 (MeCP2), and co-repressors like the retinoblastoma susceptibility protein (pRb) and Groucho-related gene proteins 1 (Grg1) and 5 (Grg5) can be found. A detailed analysis of the interaction of Grg1 with HMGB1 confirmed that the binding region contained the sequence homologous to one of the peptides identified. Our results have led us to propose that HMGB1 may play a central role in the stabilization and/or assembly of several multifunctional complexes through protein-protein interactions.
Enhanced predictability of myocardial infarction in Japanese by combined genotype analysis.

To explore the genes responsible for myocardial infarction and restenosis after percutaneous transluminal coronary angioplasty, we performed association studies of the polymorphisms of the angiotensinogen and angiotensin-converting enzyme (ACE) genes. In the first study, normotensive myocardial infarction patients (n = 103) and control subjects (n = 103), who were matched for established risk factors with the myocardial infarction patients, were randomly selected. The angiotensinogen-TT genotype (T indicates threonine instead of methionine at position 235) was more frequent in the myocardial infarction group than in the control group (P < .05). The ACE-DD genotype (D indicates a deletion polymorphism in intron 16) was also more frequent in the myocardial infarction group (P < .0001). The odds ratio estimated by the combined analysis of the angiotensinogen-TT and ACE-DD genotypes (11.2) was markedly increased compared with that estimated separately from the angiotensinogen-TT (1.75) or ACE-DD (4.43) genotype. In the second study, we investigated 91 consecutive patients with acute myocardial infarction who underwent successful direct angioplasty. Combined analysis showed that the angiotensinogen-TT genotype did not enhance the predictability of myocardial infarction from the ACE-DD genotype. In conclusion, the angiotensinogen-TT genotype is a predictor for myocardial infarction, as well as the ACE-DD genotype, and the combined analysis of the angiotensinogen-TT and ACE-DD genotypes further enhanced the predictability of myocardial infarction in Japanese, suggesting its future clinical usefulness.
Proprietary and Open Systems Adoption: A Risk-Augmented Transactions Cost Perspective.

This article presents an economic model that enables the study of incentives for business-to-business (B2B) e-procurement systems investments which permit inventory coordination and improved operational control. We focus on the information technology (IT) adoption behavior of firms in the presence of transaction costs, agency costs and information uncertainty. But we conclude that it is appropriate to rethink the prior theory and develop an extended transactions cost theory perspective, following Clemons, et al. (1993), but with the possibility of shocks included. We distinguish among three kinds of B2B eprocurement systems platforms. Proprietary platform procurement systems involve traditional electronic data interchange (EDI) technologies. Open platform procurement systems are associated with e-markets Web technology. Hybrid platforms involve elements of both. The key drivers appear to be firm size and uncertainties that derive from the inability of a buyer firm to perfectly predict final retail demand and actual supply. We find that larger firms tend to adopt costlier solutions, but rely upon procurement technologies with more certain-to-deliver value, such as proprietary EDI. Smaller firms tend to adopt less costly procurement technologies that entail greater supply uncertainties, such as open platform procurement systems. We arrive at our findings through the specification of an analytical model that captures the key elements of our perspective—transaction costs, agency costs, information uncertainty, and shocks—and specifies the conditions under which strong conclusions can be made about the likely observed equilibrium e-procurement solutions of firms. _____________________________________________________________________________________
Feature Model for Collaborative Modeling Environments

There has been a growing trend toward collaborative environments especially those utilizing browser-based interfaces which can be seen in modeling tools such as AToMPM and WebGME. In response to the growing interest in collaborative modeling, we explored existing systems and potential solutions to identify the various features relevant to collaborative modeling systems. In this paper, we detail the feature diagram resulting from our exploration of collaborative modeling systems. We also detail the features of an existing collaborative system both to illustrate the use of the diagram and further explore the features. Through this feature diagram we identify key areas for collaborative modeling systems. We hope the feature diagram will be used to guide development, analysis, and discussion around collaborative modeling systems.
On the sample complexity of randomized approaches to the analysis and design under uncertainty

In this paper, we study the sample complexity of probabilistic methods for control of uncertain systems. In particular, we show the role of the binomial distribution for some problems involving analysis and design of robust controllers with finite families. We also address the particular case in which the design problem can be formulated as an uncertain convex optimization problem. The results of the paper provide simple explicit sample bounds to guarantee that the obtained solutions meet some pre-specified probabilistic specifications.
Karyotyping urine sediment cells confirms trisomy 12 mosaicism detected at amniocentesis

A newborn is described in whom trisomy 12 mosaicism was detected prenatally at third trimester amniocentesis during the fourth pregnancy of a 34‐year‐old woman. After birth, trisomy 12 cells were found in placental tissue and in cultured urine sediment cells. A sample of cord blood and a skin biopsy revealed only normal (46,XX) cells. Both parents had a normal karyotype. After a difficult start with unexplained hypoglycaemias and convulsion equivalents, the girl is doing well at the age of 9 months: there are no signs of central motor disturbance. The importance of the use of cultured urine sediment cells in confirming chromosomal mosaicism is stressed.
Identification of VPS13C as a Galectin-12-Binding Protein That Regulates Galectin-12 Protein Stability and Adipogenesis

Galectin-12, a member of the galectin family of β-galactoside-binding animal lectins, is preferentially expressed in adipocytes and required for adipocyte differentiation in vitro. This protein was recently found to regulate lipolysis, whole body adiposity, and glucose homeostasis in vivo. Here we identify VPS13C, a member of the VPS13 family of vacuolar protein sorting-associated proteins highly conserved throughout eukaryotic evolution, as a major galectin-12-binding protein. VPS13C is upregulated during adipocyte differentiation, and is required for galectin-12 protein stability. Knockdown of Vps13c markedly reduces the steady-state levels of galectin-12 by promoting its degradation through primarily the lysosomal pathway, and impairs adipocyte differentiation. Our studies also suggest that VPS13C may have a broader role in protein quality control. The regulation of galectin-12 stability by VPS13C could potentially be exploited for therapeutic intervention of obesity and related metabolic diseases.
No-Reference Quality Assessment of Deblurred Images Based on Natural Scene Statistics

Blurring is one of the most common distortions in digital images. In the past decade, extensive image deblurring algorithms have been proposed to restore a latent clean image from its blurred version. However, very little work has been dedicated to the quality assessment of deblurred images, which may hinder further development of more advanced deblurring techniques. Motivated by this, this paper presents a no-reference quality metric for defocus deblured images based on Natural Scene Statistics (NSS). Two categories of NSS features are extracted in both the spatial and frequency domains to account for both the global and local aspects of distortions in deblurred images. Specifically, the spatial domain NSS features are used to characterize the global naturalness, and the frequency domain NSS features are used to portray the local structural distortions. All features are combined to train a support vector regression model for quality prediction of defocus deblurred images. The performance of the proposed metric is evaluated in a subjectively rated defocus deblurred image database. The experimental results demonstrate the advantages of the proposed metric over the relevant state-of-the-arts. As an application, the proposed metric is further used for benchmarking deblurring algorithms and very encouraging results are achieved.
False-negative results of conventional Papanicolaou cervical cytology in women with cervical conization

Objective：The conventional Papanicolaou smear seems to be more accurate for detecting a high-grade squamous intraepithelial lesion (HSIL) than a low-grade squamous intraepithelial lesion (LSIL). The purpose of this study was to investigate false-negative results of conventional Pap smear cytology in women with cervical conization. Methods：This study was performed in Gynecologic Oncology Clinic of the Department of Obstetrics and Gynecology at Dankook University Medical Center from July 1, 1994 to December 31, 2004. 260 women from age 22 to 75 years had undergone conventional Papanicolaou cervical cytologic test and cervical conization. Conization was performed using ‘cold-knife cone' method or ‘large electrosurgical excision procedure (LEEP) cone' method. The cervical cytology were studied in comparison with histology of conization specimens. Results：Of the 260 histologic diagnoses, there were 41 (15.8%) diagnoses of chronic cervicitis, 8 (3.1%) of CIN 1, 18 (6.9%) of CIN 2, 150 (57.7%) of CIN 3, 38 (14.6%) of SCC, 2 (0.8%) of AIS, 1 (0.4%) of ACC, and 2 (0.8%) of ASC. Pap cytology showed sensitivity of 97.9-98.2%, specificity of 4.9-6.7%, and false-negative rate of 1.8-2.2% according to the variables. Conclusion：Significantly false-negative rate of Pap cytology in women with conization was very low. And so, conventional Pap cytology is still clinically efficient for screening high-grade cervical lesions with adequate sampling technique.
Endothelial monolayers and transendothelial migration depend on mechanical properties of the substrate

Endothelial cells (ECs) line the microvasculature and constitute a barrier between the vessel lumen and surrounding tissues. ECs inform circulating immune cells of the health and integrity of surrounding tissues, recruiting them in response to pathogens and tissue damage. ECs play an active role in the transmigration of immune cells across the vessel wall. We have discovered important differences in the properties of ECs on soft hydrogel substrates of varying stiffness, in comparison to glass. Primary ECs from several human sources were tested; all formed monolayers normally on soft substrates. EC monolayers formed more mature cell‐cell junctions on soft substrates, relative to glass, based on increased recruitment of vinculin and F‐actin. EC monolayers supported transendothelial migration (TEM) on soft substrates. Immune cells, including peripheral blood lymphocytes (PBLs) and natural killer cells, showed decreasing numbers of paracellular (between‐cell) transmigration events with decreasing substrate stiffness, while the number of transcellular (through‐cell) events increased for PBLs. Melanoma cancer cells showed increased transmigration with decreased stiffness. Our findings demonstrate that endothelial monolayers respond to the mechanical properties of their surroundings, which can regulate the integrity and function of the monolayer independently from inflammatory signals. Soft hydrogel substrates are a more appropriate and physiological model for tissue environments than hard substrates, with important implications for the experimental analysis of TEM. © 2014 Wiley Periodicals, Inc.
The Wt1+/R394W Mouse Displays Glomerulosclerosis and Early-Onset Renal Failure Characteristic of Human Denys-Drash Syndrome

ABSTRACT Renal failure is a frequent and costly complication of many chronic diseases, including diabetes and hypertension. One common feature of renal failure is glomerulosclerosis, the pathobiology of which is unclear. To help elucidate this, we generated a mouse strain carrying the missense mutation Wt1 R394W, which predisposes humans to glomerulosclerosis and early-onset renal failure (Denys-Drash syndrome [DDS]). Kidney development was normal in Wt1+/R394W heterozygotes. However, by 4 months of age 100% of male heterozygotes displayed proteinuria and glomerulosclerosis characteristic of DDS patients. This phenotype was observed in an MF1 background but not in a mixed B6/129 background, suggestive of the action of a strain-specific modifying gene(s). WT1 encodes a nuclear transcription factor, and the R394W mutation is known to impair this function. Therefore, to investigate the mechanism of Wt1 R394W-induced renal failure, the expression of genes whose deletion leads to glomerulosclerosis (NPHS1, NPHS2, and CD2AP) was quantitated. In mutant kidneys, NPHS1 and NPHS2 were only moderately downregulated (25 to 30%) at birth but not at 2 or 4 months. Expression of CD2AP was not changed at birth but was significantly upregulated at 2 and 4 months. Podocalyxin was downregulated by 20% in newborn kidneys but not in kidneys at later ages. Two other genes implicated in glomerulosclerosis, TGFB1 and IGF1, were upregulated at 2 months and at 2 and 4 months, respectively. It is not clear whether the significant alterations in gene expression are a cause or a consequence of the disease process. However, the data do suggest that Wt1 R394W-induced glomerulosclerosis may be independent of downregulation of the genes for NPHS1, NPHS2, CD2AP, and podocalyxin and may involve other genes yet to be implicated in renal failure. The Wt1 R394W mouse recapitulates the pathology and disease progression observed in patients carrying the same mutation, and the mutation is completely penetrant in male animals. Thus, it will be a powerful and biologically relevant model for investigating the pathobiology of the earliest events in glomerulosclerosis.
Hedonic and Utilitarian Motivations for Physical Game Systems Use Behavior

With the recent proliferation of physical game systems in entertainment contexts, gaining a better understanding of why users are willing to utilize physical game systems has become an important topic for practitioners and academics. The current study attempts to explore the determinants of behavioral intention pertaining to the use of physical tennis games from the perspective of both hedonic and utilitarian motivations. A research model is proposed based on the existing literature. Data collected from 124 experienced players of physical tennis games are tested against the research model using the partial least squares approach. The results indicate that both perceived exercise utility and perceived enjoyment have a significant influence on behavioral intention. In addition, perceived motion-sensing, challenge, interactivity, ease of use, and design aesthetics are found to have a significant effect on perceived enjoyment. More specifically, perceived motion-sensing is observed to be the antecedent of perceived exercise utility. The findings of this study provide several important implications pertaining to both the research and practice of physical game system development and diffusion.
Predation on common tern eggs by the yellow-legged gull at the Ebro Delta*

SUMMARY: The Ebro Delta holds a large seabird community, including a common tern (Sterna hirundo) local population of 3,085 pairs in 2000 which breeds scattered in several colonies. At El Canalot colony, 1,178 (1999) and 1,156 pairs (2000) of this species bred distributed in 32 and 38 sub-colonies respectively. These sub-colonies varied in size from 1 to 223 pairs and were placed near the main breeding colonies of yellow-legged gulls (Larus cachinnans) and Audouin’s gulls (L. audouinii), which are potential egg-predators of terns. We studied egg predation during 1999 (6 sub-colonies) and 2000 (27 sub-colonies). Overall, we found that 10.6% of the nests in 1999 and 16.7% in 2000 suffered partial or total egg predation, being total in 81.1% of the predatory events. Predation was significantly higher in small sub-colonies (<11 pairs): 49.4% in 1999 and 75.5% in 2000. Only attacks from yellow-legged gulls were observed, and defence behaviour of terns was significantly more frequent against this gull species (40.5 hours of observation), suggesting that in most cases the egg predation recorded was due to this species. Probability of egg predation was significantly and negatively correlated with distance to the nearest yellow-legged gull sub-colony, although this relationship was no more significant after adjustment for subcolony size. On the other hand, distance to the nearest Audouin’s gull sub-colony did not show any effect. Our results suggest that the impact of large gulls (at least yellow-legged gulls) upon smaller seabirds breeding in the area might be important, especially when they are breeding in small sub-colonies. Further studies are needed to analyse the general impact of large gulls upon the breeding populations of other colonial bird species in the area.
Assessment of rheumatoid arthritis using a modified scoring method on digitized and original radiographs.

OBJECTIVE The results of different readers' interpretations of laser-digitized hand radiographs versus original radiographs were compared to determine the reproducibility of scoring of erosions (ERO), joint space narrowing (JSN), and their combination (ERO + JSN) in patients with rheumatoid arthritis (RA). METHODS Standardized radiographs of both hands were obtained at 2 visits (baseline and 6-24-month followup) from 30 patients with established RA. Conventional and laser-digitized (pixel sizes 50 microm and 100 microm) radiographs were scored independently by 3 experienced and trained radiologists who were blinded to the order of the visits. Scoring of radiographs was based on the validated Genant grading system. RESULTS Intertechnique (intrareader) correlation coefficients at baseline were 0.90-0.93 for scoring of ERO, 0.90-0.94 for scoring of JSN, and 0.92-0.95 for ERO + JSN; for scoring of progression between baseline and followup, these values were 0.93-0.97, 0.87-0.95, and 0.93-0.97, respectively. Interreader (intratechnique) correlation coefficients at baseline were 0.82-0.96 for scoring of ERO, 0.69-0.91 for scoring of JSN, and 0.80-0.95 for ERO + JSN; for scoring of progression between baseline and followup, these values were 0.90-0.97, 0.80-0.92, and 0.90-0.95, respectively. Intrareader (intratechnique) correlation coefficients were 0.90-0.97 for scoring of the original radiographs and 0.90-0.98 for scoring of the digitized images at 100 microm. CONCLUSION Using this modified grading system, scoring of RA progression directly from paired, high-resolution monitors of laser-digitized images of the hands provided highly reproducible results, comparable to those obtained from the original radiographs. Thus, this method may have useful applications in clinical trials involving RA.
The Calcium-Dependent Interaction between S100B and the Mitochondrial AAA ATPase ATAD3A and the Role of This Complex in the Cytoplasmic Processing of ATAD3A

ABSTRACT S100 proteins comprise a multigene family of EF-hand calcium binding proteins that engage in multiple functions in response to cellular stress. In one case, the S100B protein has been implicated in oligodendrocyte progenitor cell (OPC) regeneration in response to demyelinating insult. In this example, we report that the mitochondrial ATAD3A protein is a major, high-affinity, and calcium-dependent S100B target protein in OPC. In OPC, ATAD3A is required for cell growth and differentiation. Molecular characterization of the S100B binding domain on ATAD3A by nuclear magnetic resonance (NMR) spectroscopy techniques defined a consensus calcium-dependent S100B binding motif. This S100B binding motif is conserved in several other S100B target proteins, including the p53 protein. Cellular studies using a truncated ATAD3A mutant that is deficient for mitochondrial import revealed that S100B prevents cytoplasmic ATAD3A mutant aggregation and restored its mitochondrial localization. With these results in mind, we propose that S100B could assist the newly synthesized ATAD3A protein, which harbors the consensus S100B binding domain for proper folding and subcellular localization. Such a function for S100B might also help to explain the rescue of nuclear translocation and activation of the temperature-sensitive p53val135 mutant by S100B at nonpermissive temperatures.