Miracle-dz/UniFAR-FTUs huggingface dataset:
The long reads ahead: de novo genome assembly using the MinION

Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. The presented literature review gives an up-to-date overview of the MinION’s utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of oversight in the expanding landscape of analysis tools, as performance evaluations are outdated quickly. Now that the MinION is approaching a state of maturity, a thorough comparative benchmarking effort of de novo assembly pipelines may be at place.
Endocytosis and Enamel Formation

Enamel formation requires consecutive stages of development to achieve its characteristic extreme mineral hardness. Mineralization depends on the initial presence then removal of degraded enamel proteins from the matrix via endocytosis. The ameloblast membrane resides at the interface between matrix and cell. Enamel formation is controlled by ameloblasts that produce enamel in stages to build the enamel layer (secretory stage) and to reach final mineralization (maturation stage). Each stage has specific functional requirements for the ameloblasts. Ameloblasts adopt different cell morphologies during each stage. Protein trafficking including the secretion and endocytosis of enamel proteins is a fundamental task in ameloblasts. The sites of internalization of enamel proteins on the ameloblast membrane are specific for every stage. In this review, an overview of endocytosis and trafficking of vesicles in ameloblasts is presented. The pathways for internalization and routing of vesicles are described. Endocytosis is proposed as a mechanism to remove debris of degraded enamel protein and to obtain feedback from the matrix on the status of the maturing enamel.
Divide & Concur and Difference-Map BP Decoders for LDPC Codes

The "Divide and Concur'' (DC) algorithm, recently introduced by Gravel and Elser, can be considered a competitor to the belief propagation (BP) algorithm, in that both algorithms can be applied to a wide variety of constraint satisfaction, optimization, and probabilistic inference problems. We show that DC can be interpreted as a message-passing algorithm on a constraint graph, which helps make the comparison with BP more clear. The "difference-map'' dynamics of the DC algorithm enables it to avoid "traps'' which may be related to the "trapping sets'' or "pseudo-codewords'' that plague BP decoders of low-density parity check (LDPC) codes in the error-floor regime. We investigate two decoders for low-density parity-check (LDPC) codes based on these ideas. The first decoder is based directly on DC, while the second decoder borrows the important "difference-map'' concept from the DC algorithm and translates it into a BP-like decoder. We show that this "difference-map belief propagation'' (DMBP) decoder has dramatically improved error-floor performance compared to standard BP decoders, while maintaining a similar computational complexity. We present simulation results for LDPC codes on the additive white Gaussian noise and binary symmetric channels, comparing DC and DMBP decoders with other decoders based on BP, linear programming, and mixed-integer linear programming.
Taylor–Aris dispersion in temperature gradient focusing

Microfluidic temperature gradient focusing (TGF) uses an axial temperature gradient to induce a gradient in electrophoretic flux within a microchannel. When balanced with an opposing fluid flow, charged analytes simultaneously focus and separate according to their electrophoretic mobilities. We present a theoretical and experimental study of dispersion in TGF. We model the system using generalized dispersion analysis that yields a 1‐D convection‐diffusion equation that contains dispersion terms particular to TGF. We consider analytical solutions for the model under uniform temperature gradient conditions. Using a custom TGF experimental setup, we compare focusing measurements with the theoretical predictions. We find that the theory well represents the focusing behavior for flows within the Taylor–Aris dispersion regime.
The case for aromatase inhibitors use in Oncofertility patients. Should aromatase inhibitors be combined with gonadotropin treatment in Breast Cancer patients undergoing ovarian stimulation for fertility preservation prior to chemotherapy? A debate

Abstract Breast cancer is one of the hormone-dependent cancers that may be adversely affected by elevated oestrogen or progesterone concentrations, particularly the endocrine active (hormone receptor positive) breast cancers. Treatment for breast cancer patients aimed at fertility preservation, includes ovarian hyperstimulation, the harvest of oocytes, and subsequent cryopreservation of oocytes or embryos. Classically, gonadotrophins have been used effectively for ovulation induction, a treatment often accompanied by high blood oestrogen concentrations produced by the hyperstimulated granulosa cells. Despite the uncertainty which surrounds this issue and the lack of clear-cut clinical evidence, it is still of major concern that these ensuing high hormone levels might be associated with a high risk of recurrence of the cancer. A growing number of clinical studies have strongly suggested the benefits of using aromatase inhibitors in infertility treatment, both as single agents or as adjuncts to FSH-containing ovulation induction regimes in reproductive medicine. Combining gonadotrophins with aromatase inhibitors would augment the stimulation effect, with a reduced increase in serum concentrations of estradiol. We propose to open a debate over the use of aromatase inhibitors in combination with FSH in ovulation induction treatment of breast cancer oncofertility patients. As the safety of aromatase inhibitors such as letrozole has recently been demonstrated in several studies, and there is growing concern over the possible detrimental effects of high estradiol levels on breast cancer cells (at least in mouse models), the co-administration of letrozole in these patients would reduce both the high supraphysiologic serum levels of estradiol and the intratumoral in situ production of oestrogen. However, since it is unlikely that a well-founded evidence-based justification of this treatment will be formulated in the near future, based on well-designed prospective randomised controlled trials, we advocate a wider use of aromatase inhibitors in combination with gonadotrophins in breast cancer patients, especially those with hormone-receptor-positive tumours.
PET Analysis of Dopaminergic Neurodegeneration in Relation to Immobility in the MPTP-Treated Common Marmoset, a Model for Parkinson’s Disease

Background Positron Emission Tomography (PET) measurement was applied to the brain of the common marmoset, a small primate species, treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). The marmoset shows prominent Parkinson’s disease (PD) signs due to dopaminergic neural degeneration. Recently, the transgenic marmoset (TG) carrying human PD genes is developing. For phenotypic evaluations of TG, non-invasive PET measurement is considered to be substantially significant. As a reference control for TG, the brain of the MPTP-marmoset as an established and valid model was scanned by PET. Behavioral analysis was also performed by recording locomotion of the MPTP-marmoset, as an objective measure of PD signs. Methodology/Principal Findings Marmosets received several MPTP regimens (single MPTP regimen: 2 mg/kg, s.c., per day for 3 consecutive days) were used for PET measurement and behavioral observation. To measure immobility as a central PD sign, locomotion of marmosets in their individual living cages were recorded daily by infrared sensors. Daily locomotion counts decreased drastically after MPTP regimens and remained diminished for several months or more. PET scan of the brain, using [11C]PE2I as a ligand of the dopamine (DA) transporter, was performed once several months after the last MPTP regimen. The mean binding potential (BPND) in the striatum (putamen and caudate) of the MPTP-marmoset group was significantly lower than that of the MPTP-free control group (n = 5 for each group). In the MPTP-marmosets, the decrease of BPND in the striatum closely correlated with the decrease in locomotion counts (r = 0.98 in putamen and 0.91 in caudate). Conclusion/Significance The present characterization of neural degeneration using non-invasive PET imaging and of behavioral manifestation in the MPTP marmoset mimics typical PD characteristics and can be useful in evaluating the phenotype of TG marmosets being developed.
The Natural History of Globus Pharyngeus

Globus pharyngeus is a common disorder and accounts for 5% of all ENT referrals. Objectives. To evaluate the role of barium swallow and endoscopy in these patients, to ascertain the incidence, if any, of aerodigestive tract malignancy in this group and to assess the natural evolution of globus pharyngeus. Materials and Methods. Seventy-nine patients underwent barium swallow and rigid oesophagoscopy for globus pharyngeus between January 2005 and October 2008. Fifty-five patients were contacted by phone on average 5 years and 3 months after intervention and asked if their symptoms still persisted. Twenty-four patients were uncontactable or lost to followup, three patients were deceased, two of cardiac related disease and one of renal failure. Results. The majority of patients, 36 of 55 (65%), had a normal barium swallow. Forty-five of 55 (82%) of patients had normal rigid endoscopies. Thirty-one of 55 (56%) patients were at an average followup time of 5 years and 3 months. No patient developed a malignant lesion. Conclusion. Globus pharyngeus is a relatively common but benign condition of indeterminate origin. Our study demonstrates that many of these patients spontaneously improve with time.
An experiment in reducing cellular base station power draw with virtual coverage

Lack of access to cellular service often goes hand-in-hand with lack of access to power. For example, the GSM Association estimates that 95% of people living without cellular access in East Africa also lack access to grid power. This situation forces cellular network operators to build out power infrastructure along with their network infrastructure, dramatically increasing costs. While numerous equipment providers offer "low-power" GSM Base Stations (BTS) for use with renewable energy sources, these have a power floor of roughly 70W, which still necessitates a large upfront expenditure. The naïve solution to this problem is duty-cycling---simply turning off the equipment for portions of the day, usually at night. This commonly-adopted approach prevents important use cases such as all-hours emergency calling. Recently, we proposed a technique called virtual coverage to provide on-demand cellular coverage by introducing a "sleep" mode for cellular equipment. The solution turns off the BTS during low-utilization periods, but allows users to power the system back on using specialized autonomous radios if they need to communicate. Incoming communications also wake the BTS, facilitating two-way correspondence. While a potential solution, no real-world deployments have yet validated virtual coverage. The core goal of this work is do just that; we utilize virtual coverage to provide both low power consumption and on-demand access in a real cellular network during a six-month deployment in rural Papua, Indonesia. We demonstrate that the system was used and understood by customers, with more than half of subscribers using the system during "night" (i.e., on-battery) hours, making 730 outbound and receiving 755 inbound communications. Our scheme also allowed the BTS to be in low-power mode for 87% of night hours, reducing night power draw by 56.6%. We believe these results demonstrate that virtual coverage is a viable solution for reducing power draw in rural cellular networks.
Cooperative MIMO-OFDM communications: Receiver design for Doppler-distorted underwater acoustic channels

Multiple-input multiple-output (MIMO) communications based on orthogonal frequency division multiplexing (OFDM) are considered for improving the performance and bandwidth utilization of underwater acoustic systems in which cooperation is possible between distributed transmitters. The major challenge in such a framework - and the principal difference from the traditional case where multiple transmitters are co-located - is the fact that distributed transmitter-receiver pairs may experience significantly different Doppler distortion (e.g. two vehicles moving in different directions with respect to the receiver). The conventional approach of front-end resampling that corrects for a common Doppler scaling will then fail, rendering a post-FFT signal that is contaminated by transmitter-specific inter-carrier interference. To counteract this problem, we propose a front-end receiver structure that utilizes multiple resampling branches, each followed by FFT demodulation. As a result, a set of sufficient statistics are acquired, which are subsequently processed using custom-designed, linear or nonlinear detection schemes. Numerical results illustrate significant performance improvements as compared to the conventional, single-resampling schemes.
Variations of Surveillance Practice for Patients with Bone Sarcoma: A Survey of Australian Sarcoma Clinicians

Introduction. After treatment, bone sarcoma patients carry a high chance of relapse and late effects from multimodal therapy. We hypothesize that significant variation in surveillance practice exists between pediatric medical oncology (PO) and nonpediatric medical oncology (NP) sarcoma disciplines. Methods. Australian sarcoma clinicians were approached to do a web based survey that assessed radiologic surveillance (RS) strategies, late toxicity assessment, and posttreatment psychosocial interventions. Results. In total, 51 clinicians responded. No differences were identified in local disease RS. In metastatic disease response assessment, 100% of POs (23/23) and 93% of NPs (24/26) conducted CT chest. However, this was more likely to occur for NPs in the context of a CT chest/abdomen/pelvis (NP: 10/26; PO: 1/23; p = 0.006). POs were more likely to use CXR for RS (p = 0.006). POs showed more prescriptive intensity in assessment of heart function (p = 0.001), hearing (p < 0.001), and fertility (p = 0.02). POs were more likely to deliver written information for health maintenance/treatment summary (p = 0.04). The majority of respondents described enquiring about psychosocial aspects of health (n = 33/37, 89%), but a routine formal psychosocial screen was only used by 23% (n = 6/26). Conclusion. There is high variability in bone sarcoma surveillance between PO and NP clinicians. Efforts to harmonize approaches would allow early and late effects recognition/intervention and facilitate improved patient care/transition and research.
Measurements of Disordered Flows Distal to Subtotal Vascular Stenoses in the Thoracic Aortas of Dogs

Instantaneous blood velocity measurements employing a constant temperature hot film anemometer were obtained in the region distal to externally enforced, subtotal vascular stenoses in the descending thoracic aortas of anesthetized dogs. Our objectives were to determine alterations in velocity waveforms and energy spectra as the degree of stenosis was increased. We paid particular attention to distinguishing features of the flow which were characteristic of turbulence. Our results indicate that, for the vessels studied, disturbances in the velocity waveforms occur for very minor localized constrictions. The energy spectra follow certain similarity parameters within a restricted region of the distal velocity field. For severe stenoses relatively high levels of energy exist in frequency ranges which previously have been found to produce poststenotic dilation. The measurements suggest that velocity waveforms and energy spectra provide a very early clue to the existence of localized occlusive vascular disease in larger vessels and that, within a limited region distal to a stenosis, the degree of constriction may be estimated by similarity analysis of the energy spectra.
The Role of Data Cap in Optimal Two-part Network Pricing

Internet services are traditionally priced at flat rates; however, many Internet service providers (ISPs) have recently shifted towards two-part tariffs where a data cap is imposed to restrain data demand from heavy users and usage over the data cap is charged based on a per-unit fee. Although the two-part tariff could generally increase the revenue for ISPs and has been supported by the FCC chairman, the role of data cap and its revenue-optimal and welfare-optimal pricing structures are not well understood. In this paper, we study the impact of data cap on the optimal two-part pricing schemes for congestion-prone service markets, e.g., broadband or cloud services. We model users' demand and preferences over pricing and congestion alternatives and derive the market share and congestion of service providers under a market equilibrium. Based on the equilibrium model, we characterize the two-part structures of the revenue-optimal and welfare-optimal pricing schemes. Our results reveal that 1) the data cap provides a mechanism for ISPs to transition from flat-rate to pay-as-you-go type of schemes, 2) with growing data demand and network capacity, the revenue-optimal pricing moves towards usage-based schemes with diminishing data caps, and 3) the structure of the welfare-optimal tariff comprises lower fees and data cap than those of the revenue-optimal counterpart, suggesting that regulators might want to promote usage-based pricing but regulate the per-unit fees. Our results could help providers design revenue-optimal pricing schemes and guide regulatory authorities to legislate desirable regulations.
Prevalence of Overweight, Obesity, and Associated Diseases among Outpatients in a Public Hospital

Background The prevalence of obesity is increasing and may be particularly high among indigent public hospital patients. The purpose of this study was to determine the prevalence of obesity and its associated chronic medical conditions among outpatients at Louisiana State University Health Sciences Center–Shreveport, an urban tertiary health center that serves a mostly black, indigent population. Methods A cross-sectional survey was conducted on 1,507 primary care patients. Age, sex, weight, height, and diagnoses were recorded, and body mass index (BMI) was calculated. Results Eighty-one percent of patients were overweight or obese and 75% had one or more obesity-associated conditions. Higher BMI was significantly associated with increased prevalence of obesity-related diseases (P < 0.001) even when adjusted for age and sex. Conclusion Overweight and obesity rates at this public hospital are alarming and may indicate a problem in public hospitals across the United States. The process and structure of care for overweight and obese patients need to be evaluated, and training for residents needs to address this problem.
Aberrant epithelial-mesenchymal Hedgehog signaling characterizes Barrett's metaplasia.

BACKGROUND & AIMS The molecular mechanism underlying epithelial metaplasia in Barrett's esophagus remains unknown. Recognizing that Hedgehog signaling is required for early esophageal development, we sought to determine if the Hedgehog pathway is reactivated in Barrett's esophagus, and if genes downstream of the pathway could promote columnar differentiation of esophageal epithelium. METHODS Immunohistochemistry, immunofluorescence, and quantitative real-time polymerase chain reaction were used to analyze clinical specimens, human esophageal cell lines, and mouse esophagi. Human esophageal squamous epithelial (HET-1A) and adenocarcinoma (OE33) cells were subjected to acid treatment and used in transfection experiments. Swiss Webster mice were used in a surgical model of bile reflux injury. An in vivo transplant culture system was created using esophageal epithelium from Sonic hedgehog transgenic mice. RESULTS Marked up-regulation of Hedgehog ligand expression, which can be induced by acid or bile exposure, occurs frequently in Barrett's epithelium and is associated with stromal expression of the Hedgehog target genes PTCH1 and BMP4. BMP4 signaling induces expression of SOX9, an intestinal crypt transcription factor, which is highly expressed in Barrett's epithelium. We further show that expression of Deleted in Malignant Brain Tumors 1, the human homologue of the columnar cell factor Hensin, occurs in Barrett's epithelium and is induced by SOX9. Finally, transgenic expression of Sonic hedgehog in mouse esophageal epithelium induces expression of stromal Bmp4, epithelial Sox9, and columnar cytokeratins. CONCLUSIONS Epithelial Hedgehog ligand expression may contribute to the initiation of Barrett's esophagus through induction of stromal BMP4, which triggers reprogramming of esophageal epithelium in favor of a columnar phenotype.
Deregulation of ARID1A, CDH1, cMET and PIK3CA and target-related microRNA expression in gastric cancer

Genetic and epigenetic alterations play an important role in gastric cancer (GC) pathogenesis. Aberrations of the phosphatidylinositol-3-kinase signaling pathway are well described. However, emerging genes have been described such as, the chromatin remodeling gene ARID1A. Our aim was to determine the expression levels of four GC-related genes, ARID1A, CDH1, cMET and PIK3CA, and 14 target-related microRNAs (miRNAs). We compared mRNA and miRNA expression levels among 66 gastric tumor and normal adjacent mucosa samples using quantitative real-time reverse transcription PCR. Moreover, ARID1A, cMET and PIK3CA protein levels were assessed by immunohistochemistry (IHC). Finally, gene and miRNAs associations with clinical characteristics and outcome were also evaluated. An increased cMET and PIK3CA mRNA expression was found in 78.0% (P = 2.20 × 10−5) and 73.8% (P = 1.00 × 10−3) of the tumors, respectively. Moreover, IHC revealed that cMET and PIK3CA expression was positive in 63.6% and 87.8% of the tumors, respectively. Six miRNAs had significantly different expression between paired-samples, finding five up-regulated [miR-223-3p (P = 1.65 × 10−6), miR-19a-3p (P = 1.23 × 10−4), miR-128-3p (P = 3.49 × 10−4), miR-130b-3p (P = 1.00 × 10−3) and miR-34a-5p (P = 4.00 × 10−3)] and one down-regulated [miR-124-3p (P = 0.03)]. Our data suggest that cMET, PIK3CA and target-related miRNAs play an important role in GC and may serve as potential targets for therapy.
On Unbiased Sampling for Unstructured Peer-to-Peer Networks

This paper presents a detailed examination of how the dynamic and heterogeneous nature of real-world peer-to-peer systems can introduce bias into the selection of representative samples of peer properties (e.g., degree, link bandwidth, number of files shared). We propose the metropolized random walk with backtracking (MRWB) as a viable and promising technique for collecting nearly unbiased samples and conduct an extensive simulation study to demonstrate that our technique works well for a wide variety of commonly-encountered peer-to-peer network conditions. We have implemented the MRWB algorithm for selecting peer addresses uniformly at random into a tool called ion-sampler. Using the Gnutella network, we empirically show that ion-sampler yields more accurate samples than tools that rely on commonly-used sampling techniques and results in dramatic improvements in efficiency and scalability compared to performing a full crawl.