Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of 18 polymorphic microsatellite markers for Vinca minor (Apocynaceae) via 454 pyrosequencing1

Premise of the study: Polymorphic microsatellite markers were developed in Vinca minor (Apocynaceae) to evaluate the level of clonality, population structure, and genetic diversity of the species within its native and introduced range. Methods and Results: A total of 1371 microsatellites were found in 43,565 reads from 454 pyrosequencing of genomic V. minor DNA. Additional microsatellite loci were mined from publicly available cDNA sequences. After several rounds of screening, 18 primer pairs flanking di-, tri-, or tetranucleotide repeats were identified that revealed high levels of genetic diversity in two native Italian populations, with two to 11 alleles per locus. Clonal growth predominated in two populations from the introduced range in Germany. Five loci successfully cross-amplified in three additional Vinca species. Conclusions: The novel polymorphic microsatellite markers are promising tools for studying clonality and population genetics of V. minor and for assessing the historical origin of Central European populations.
Node Aggregation for Enhancing PageRank

In this paper, we study the problem of node aggregation under different perspectives for increasing PageRank of some nodes of interest. PageRank is one of the parameters used by the search engine Google to determine the relevance of a web page. We focus our attention to the problem of finding the best nodes in the network from an aggregation viewpoint, i.e., what are the best nodes to merge with for the given nodes. This problem is studied from global and local perspectives. Approximations are proposed to reduce the computation burden and to overcome the limitations resulting from the lack of centralized information. Several examples are presented to illustrate the different approaches that we propose.
An accurate step detection algorithm using unconstrained smartphones

In recent years, mobile device (e.g., smartphone, tablet and etc.) equipped with various inertial sensors is increasingly popular in daily life, and a large number of mobile applications have been developed based on such built-in inertial sensors. In particular, detecting and counting steps is a prerequisite for many applications, such as smart healthcare, smart home, tracking and location, and etc., and thus has attained much attention. Peak detection is known to be one of the simplest and most efficient solutions in this field, but suffers from the drift in the orientation and position of the device if it is not tightly fixed on the human's body. In this paper, we present a novel method to accurately detect and count steps of a human who carries on a smartphone in an unconstrained manner. To be specific, the proposed method fuses the signals from the accelerometer, magnetometer and gyroscope of the smartphone to transform the device reference frame to the earth reference frame, and then employs the vertical acceleration to implement the peak detection algorithm. Extensive simulations are carried out and confirm that the proposed method is more robust than the existing algorithms.
microRNA control of cell-cell signaling during development and disease

MicroRNAs (miRNAs) are critical post-transcriptional regulators that may collectively control a majority of animal genes. With thousands of miRNAs identified, a pressing challenge is now to understand their specific biological activities. Many predicted miRNA:target interactions only subtly alter gene activity. It has consequently not been trivial to deduce how miRNAs are relevant to phenotype, and by extension, relevant to disease. We note that the major signal transduction cascades that control animal development are highly dose-sensitive and frequently altered in human disorders. On this basis, we hypothesize that developmental cell signaling pathways represent prime candidates for mediating some of the major phenotypic consequences of miRNA deregulation, especially under gain-of-function conditions. This perspective reviews the evidence for miRNA targeting of the major signaling pathways, and discusses its implications for how aberrant miRNA activity might underlie human disease and cancer.
A 1-V 3.5-mW CMOS switched-opamp quadrature IF circuitry for Bluetooth receivers

Based on only half-delay switched-capacitor integrators, a 7/sup th/-order IF-filter and a 3/sup rd/-order /spl Sigma//spl Delta/ modulator using a novel noise-shaping extension technique are implemented for a Bluetooth receiver in a 0.35-/spl mu/m CMOS process. At a 1-V supply, the quadrature IF circuitry achieves a measured IIP3 of -3 dBm at a nominal gain of 24 dB through a 48-dB variable-gain control with a power dissipation of 3.5 mW.
An Alternate Load Distribution Scheme in DHTs

This paper analyzes, compares and looks at tradeoffs in different load distribution schemes for consistent hashing in DHTs(distributed hash tables). Different traffic patterns, including an adversarial pattern, were constructed to test the load distribution. A simulator was made for each load distribution scheme and the load on each node was recorded for each traffic pattern. It was shown that increasing the number of consistent hash rings doesn't change the load distribution characteristics of the DHT in simple traffic scenarios, but in the case of adversarial traffic, increasing the number of hash rings leads to an improvement of around 15% in the load distribution statistics.
Infrared Densitometry: A Fast and Non-Destructive Method for Exact Stratum Corneum Depth Calculation for in vitro Tape-Stripping

The investigation of drug penetration into the stratum corneum (SC) by tape-stripping requires an accurate measure of the amount of SC on each tape-strip in order to determine the depth inside the SC. This study applies infrared densitometry (IR-D) to in vitro tape-stripping using the novel Squame Scan® 850A. The device had recently been shown to provide accurate measurements of the SC depth for tape-stripping in vivo. Furthermore, the suitability of IR-D for determining the endpoint of tape-stripping, i.e. complete SC removal, was tested. The SC depth was computed from the IR-D data of sequential tape-strips and compared to the results of a protein assay as gold standard. IR-D provided accurate depth results both for freshly excised skin and for skin stored frozen for up to 3 months. In addition, the lower limit of quantification of IR-D indicates the complete removal of the SC (less than 5% of the total SC remaining) and can be used for adjusting the number of tapes applied in situ. Therefore, IR-D is an accurate, fast and non-destructive method for SC depth determination.
Murine Cytomegalovirus US22 Protein pM140 Protects Its Binding Partner, pM141, from Proteasome-Dependent but Ubiquitin-Independent Degradation

ABSTRACT Stable assembly of murine cytomegalovirus (MCMV) virions in differentiated macrophages is dependent upon the expression of US22 family gene M140. The M140 protein (pM140) exists in complex with products of neighboring US22 genes. Here we report that pM140 protects its binding partner, pM141, from ubiquitin-independent proteasomal degradation. Protection is conferred by a stabilization domain mapping to amino acids 306 to 380 within pM140, and this domain is functionally independent from the region that confers binding of pM140 to pM141. The M140 protein thus contains multiple domains that collectively confer a structure necessary to function in virion assembly in macrophages.
Diminished Hepatic Response to Fasting/Refeeding and Liver X Receptor Agonists in Mice with Selective Deficiency of Sterol Regulatory Element-binding Protein-1c*

Two treatments, fasting/refeeding and administration of liver X receptor (LXR) agonists, elevate the mRNA for sterol regulatory element-binding protein-1c (SREBP-1c) and enhance lipid synthesis in liver. These treatments do not affect the mRNA for SREBP-1a, an alternative transcript from the same gene. Through homologous recombination, we eliminated the exon encoding SREBP-1c from the mouse genome, leaving the SREBP-1a transcript intact. On a normal diet, livers ofSREBP-1c −/− mice manifested reductions in multiple mRNAs encoding enzymes of fatty acid and triglyceride synthesis, including acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS). In contrast, SREBP-1c −/−livers showed a compensatory increase in hepatic SREBP-2 mRNA, accompanied by increased mRNA levels for cholesterol biosynthetic enzymes. In fasted/refed animals, ACC and FAS mRNAs rose, but not to the same extent as in wild-type livers. The refeeding-induced increase in SREBP-1c −/− mice was greater than in mice lacking SREBP cleavage-activating protein (SCAP), in which all nuclear SREBPs are absent. Thus, SREBP-2 and/or SREBP-1a can substitute partially for SREBP-1c in permitting an insulin-mediated increase in ACC and FAS mRNAs. In contrast, mRNAs for several other lipogenic enzymes (glucose-6-phosphate dehydrogenase, malic enzyme, glycerol-3-phosphate acyltransferase, and stearoyl-CoA desaturase-1) showed a complete failure of the normal inductive response to refeeding, indicating specific reliance on SREBP-1c. Moreover, these mRNAs, as well as multiple other lipogenic mRNAs, showed a markedly blunted response to the LXR agonist T090137, indicating an essential role of SREBP-1c in the LXR response.
Diffusion tensor imaging fiber tractography for evaluating diffuse axonal injury

Patients with Diffuse axonal injury (DAI) frequently exhibit cognitive disorders chronically. Radiologic recognition of DAI can help understand the clinical syndrome and to make treatment decisions. However, CT and conventional MRI are often normal or demonstrate lesions that are poorly related to the cognitive disorders. Recently, diffusion tensor imaging (DTI) fiber tractography has been shown to be useful in detecting various types of white matter damage. The aim of this study was to evaluate the feasibility of using DTI fiber tractography to detect lesions in DAI patients, and to correlate the DAI lesions with the cognitive disorders. We investigated two patients with chronic DAI. Both had impaired intelligence, as well as attention and memory disorders that restricted their activities of daily living. In both patients, DTI fiber tractography revealed interruption of the white matter fibers in the corpus collosum and the fornix, while no lesions were found on conventional MRI. The interruption of the fornix which involves the circuit of Papez potentially correlates with the memory disorder. Therefore, DTI fiber tractography may be a useful technique for the evaluation of DAI patients with cognitive disorders.
Plz Urgent Help Needed!1!! - Aspects of On-line Knowledge Sharing in End-user Development Support

In this paper the knowledge sharing and contributing in on-line communities, specifically one for providing end-user development support is examined. The focus is on the knowledge seeker/contributor interactions and how the seeker can impact on the quality of support. Knowledge seekers post threads asking questions and contributors answer them. Knowledge contributors were asked their attitude towards the support interaction, e.g. the impact of the topic, the importance of presentation and content and knowledge seeker actions. From the answers a set of guidelines for best practice knowledge seeker actions is constructed that outlines what a knowledge seeker can do to improve the chance of getting help.
Lef1 expression in fibroblasts maintains developmental potential in adult skin to regenerate wounds

Scars are a serious health concern that impacts the clinical outcome and long-term well-being of burn victims and individuals with genetic skin conditions associated with wound healing. In this study using mouse as the model, we identify regenerative factors in neonatal skin that will transform adult skin to regenerate instead of repairing wounds with a scar, without perturbing normal development and homeostasis. We utilized single-cell RNA-sequencing (scRNA-seq) to probe unsorted cells from Regenerating, Scarring, Homeostatic, and Developing skin. Our results revealed a transient regenerative cell type in Developing skin, called papillary fibroblasts, which are defined by the expression of a canonical Wnt transcription factor Lef1. Tissue specific ablation of Lef1 inhibited skin regeneration. Importantly, ectopic expression of Lef1 in dermal fibroblasts did not disrupt development and aging, but primed adult skin to undergo enhanced regeneration. Here, we reveal the possibility of transferring the regenerative abilities of neonatal skin to adult tissue by expressing Lef1 in dermal fibroblasts. Finally, we have generated an expandable web resource with a search function to display gene expression in the context of our scRNA-seq data (https://skinregeneration.org/).
Prrx1b directs pro-regenerative fibroblasts during zebrafish heart regeneration

Rationale The human heart loses millions of cardiomyocytes after an ischemic injury, but is unable to regenerate the lost tissue. Instead, the injured human heart is repaired by pro-fibrotic fibroblasts that form a large permanent scar. In contrast, the injured zebrafish heart regenerates efficiently without the formation of a permanent scar. While fibroblasts have been shown to be indispensable for zebrafish heart regeneration, very little is known about the mechanisms balancing the fibrotic and regenerative response. A better understanding of these mechanisms could lead to the discovery of novel therapeutic strategies to reduce fibrosis and promote heart regeneration. Objective To identify novel mechanisms that regulate the balance between cardiac fibrosis and scar-free regeneration. Methods and Results Using a genetic approach, we first show that zebrafish prrx1b loss-of-function mutants display reduced cardiomyocyte proliferation and impaired heart regeneration. Using a lineage tracing approach, we show that Prrx1b is expressed in tcf21+ epicardial-derived cells localizing around and inside the injured area. Next, we used a single cell RNA-sequencing approach on sorted tcf21+ cells isolated from injured prrx1b-/- and wild-type hearts and identified two distinct fibroblast populations. With combined bioinformatic and histological analysis we found that prrx1b-/- hearts contain an excess of pro-fibrotic fibroblasts that produce TGF-β ligands and collagens, while fewer pro-regenerative Nrg1-expressing fibroblasts are formed. Furthermore, by injecting recombinant NRG1 in prrx1b-/- fish we were able to rescue their cardiomyocyte proliferation defect. Finally, using cultured human fetal epicardial cells and siRNA mediated knock-down of PRRX1 we found that PRRX1 is required for NRG1 induction in human epicardial-derived cells. Conclusions Prrx1b in the injured heart restricts fibrosis and stimulates regeneration by directing epicardial-derived cells towards a pro-regenerative Nrg1-producing fibroblast state.
DNA glycosylase NEIL2 prevents Fusobacterium-mediated inflammation and DNA damage in colonic epithelial cells

Colorectal cancer (CRC) is the third most prevalent and deadly cancer. Approximately, 15-20 % of CRCs display microsatellite instability (MSI); however, the majority (80–85%) of cases are sporadic and known as microsatellite stable (MSS). Several recent studies indicated that infection and uncontrolled inflammation initiate DNA damage and lead to cancer progression. One of the major microbes, Fusobacterium nucleatum (Fn) is highly associated with CRC, but the role of DNA repair in microbe-associated CRC has been largely unknown. Here we show that NEIL2, an oxidized base-specific DNA glycosylase, is significantly downregulated among all the key DNA repair proteins involved in various DNA repair pathways, after infection of Fn with stem-cell-based enteroid-derived monolayers (EDMs) of murine and human healthy subjects. Furthermore, following Fn infection, NEIL2-null mouse-derived EDMs showed significantly higher level of DNA damage, including double strand breaks, and inflammatory cytokines. Murine CRC model also showed downregulation of the NEIL2 transcript and accumulation of DNA damage. Importantly, analysis of publicly available transcriptomic data showed that the downregulation of NEIL2 is specific for MSS compared to MSI CRCs. We thus conclude that the pathogenic bacterial infection-induced downregulation of NEIL2, and consequent accumulation of DNA damage, play critical roles in the progression of CRC.
Detection and characteristics of individuals with a very long duration of untreated psychosis in an early intervention for psychosis service

Early intervention (EI) services for psychosis aim to reduce the duration of untreated psychosis (DUP) with intensive large‐scale multi‐focus initiatives, including public awareness campaigns. As a consequence of this approach, individuals with a very long DUP who might have otherwise remained undiagnosed may come to medical attention. The aim of this study was to investigate if an EI service detected additional cases of individuals with a first‐episode psychosis (FEP) with a very long DUP and identify demographic and clinical characteristics associated with a very long DUP.
Impact of vanB vancomycin-resistant enterococcal bacteraemia analysed as a time-varying covariate on length of hospital stay

SUMMARY The impact of vanB vancomycin-resistant enterococci (VRE) bacteraemia on length of stay (LOS) in hospital, after adjusting for the time-varying nature of enterococcal bacteraemia (variable onset of bacteraemia post-admission), is unknown. Survival analyses (time-varying Cox and competing risks regression) were performed on vanB VRE bacteraemia patients, matched 1:1 with vancomycin-susceptible enterococci bacteraemia patients to determine the factors associated with LOS in these patients. In Cox regression analysis, vanB VRE bacteraemia, intensive-care-unit admission, Charlson co-morbidity index score ⩾4, and an increase in the time to receive appropriate antibiotics were associated with prolonged LOS. Competing risks regression which accounts for the influence of in-patient mortality on the ability to observe the event discharge alive from hospital suggests that, vanB VRE bacteraemia was not significantly associated with prolonged LOS. For the first time, the rate of discharge from hospital in patients with vanB VRE bacteraemia has been quantified.
Temporal hierarchy converges with spatial hierarchy: Intrinsic neural timescales follow core-periphery organization

The human cortex exhibits intrinsic neural timescales that shape a temporal hierarchy. Whether this temporal hierarchy follows the spatial hierarchy of core-periphery organization remains an open issue. Using Magnetoencephalography data from the Human Connectome Project, we investigate intrinsic neural timescales during rest and task states; we measure the autocorrelation window in short (ACW-50) and, introducing a novel variant, long (ACW-0) windows. We demonstrate longer ACW-50 and ACW-0 in networks located at the core compared to those at the periphery with rest and task states showing a high ACW correlation. Calculating rest-task differences, i.e., subtracting the shared core-periphery organization, reveals task-specific ACW changes in distinct networks. Finally, employing kernel density estimation, machine learning, and simulation, we demonstrate that ACW-0 exhibits better prediction in classifying a region’s time window as core or periphery. Overall, our findings provide fundamental insight into how the human cortex’s temporal hierarchy converges with its spatial core-periphery hierarchy.
Three Dimensional Numerical Simulation and Modeling of Small Geometry Fully Depleted SOI MOSFET

Silicon-On-Insulator (SOI MOSFET), based on the numerical solution of three dimensional Poisson's equation is presented in this paper. Liebmann's iteration method was used to solve the three dimensional Poisson's equation with necessary boundary conditions. By using the solution of the Poisson's equation potential profile, electric field profile, mobility profile, transfer characteristics and transconductance Vs gate voltage characteristics were calculated and plotted. applicable to any 2 dimensional and 3 dimensional problems. Therefore it is worthwhile to realize a device using numerical modeling to get a more accurate result than that of an analytical model. The 3-D Poisson's Equation is numerically solved by using Liebman's iteration. The boundary conditions used for the solution of Poisson's equation are applicable only for bulk MOSFETs. The surface potential for the SOI MOSFET can be obtained from this solution of three dimensional Poisson's equation. The electric field and mobility is also calculated based on the surface potential. David Esseni (9) described a mobility model for SOI MOSFET using solution of 1D Poisson's equation. A short- channel threshold voltage model for FDSOI MOSFET is developed using a quasi-two-dimensional approach similar to those used for modeling threshold voltage, substrate current, and other hot-electron phenomena in bulk MOSFET's are also discussed in (10)-(14).
Asymptotic performance of collaborative spectrum sensing under correlated log-normal shadowing

Collaborative spectrum sensing enables opportunistic unlicensed access to the unused portions of the licensed spectrum. We characterize the performance degradation of collaborative sensing due to correlated shadowing by deriving a lower-bound on the probability of missing the opportunities for unlicensed access. Moreover, we evaluate the effective number of collaborating users in terms of the distance spread of the sensing network and the characteristics of the propagation environment. This has practical implications in terms of protocol design as having a few number of users collaborate over a large distance may be more effective than a dense sensing network confined to a small area
Analysis on acoustic similarities between Tamil and English phonemes using product of likelihood-Gaussians for an HMM-based mixed-language synthesizer

A mixed-language (polyglot) synthesizer is one that synthesizes intelligible multilingual speech with a single speaker's voice with appropriate pronunciations. Two main requirements of a mixed-language synthesizer are that (i) the transition from one language to another (language switching) and (ii) the influence of one language on another should not be perceivable. In this regard, in [1], while developing a bilingual text-to-speech (TTS) system for Mandarin and English, the minimum Kullback-Leibler divergence(KLD) criterion, applied state-wise to the context-independent hidden Markov models(HMMs) is used to cluster the states of acoustically similar phonemes across the two languages. In the current work, using context-independent HMMs trained separately for two languages, namely, Tamil and English, an attempt has been made to find the acoustically similar phonemes using product of Gaussians (PoG) in the log-likelihood space. A speech corpus, with Tamil and English data, uttered by the same speaker, is used for this task. The quality of the speech synthesized by the mixed-language synthesizer is assessed subjectively, and the mean opinion score of 3.49 is obtained when acoustically similar phonemes alone are merged. In addition, analyses are carried out to find the amount of language switching and the influence of one language on the other.