Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic and vibrational properties of two-dimensional materials constructed from graphene and molecular components

In the first part of this dissertation, We study the effects of electron-phonon coupling on the electronic properties of two-dimensional graphene-based materials and molecular lattices. We develop a theoretical model of magneto-phonon resonances in graphene under high magnetic fields, for phonons at both Gamma and K points. Multiphonon excitations in molecular lattices are treated within the cumulant expansion, leading to an accurate description of phonon satellite structures in tunneling experiments. The second half of this dissertation deals with the electronic structure of graphene-based materials and two-dimensional electron gases under external long wavelength potential variations. We show how a graphene-like electronic structure can be created in molecular lattices self-assembled on metal surfaces. We show how velocity renormalization, new Dirac points, and band gap openings can occur when modulated electric and magnetic fields are applied to graphene or bilayer graphene.
Interaction phenomena in graphene seen through quantum capacitance

Capacitance measurements provide a powerful means of probing the density of states. The technique has proved particularly successful in studying 2D electron systems, revealing a number of interesting many-body effects. Here, we use large-area high-quality graphene capacitors to study behavior of the density of states in this material in zero and high magnetic fields. Clear renormalization of the linear spectrum due to electron–electron interactions is observed in zero field. Quantizing fields lead to splitting of the spin- and valley-degenerate Landau levels into quartets separated by interaction-enhanced energy gaps. These many-body states exhibit negative compressibility but the compressibility returns to positive in ultrahigh B. The reentrant behavior is attributed to a competition between field-enhanced interactions and nascent fractional states.
Physicochemical analysis of Gelatin extracted from mechanically deboned chicken meat (mdcm) residue

Purpose: Mechanically Deboned Chicken Meat Residue (MDCMR) is a waste product from chicken processing. Gelatin is water soluble protein mostly present in animals. Methodology: Gelatin extracted from Mechanically Deboned Chicken Meat Res- idue by combination alkaline-acid extraction process. Highest yield of gelatin extracted (%w/w) at temperature 80°C (16.03%) compare with gelatin extract- ed at 60°C (5.96%) and 70°C (14.19%). Findings: Proximate analysis of MDCMR showed the protein, moisture, lipid and ash content were 17.77±0.10%, 62.26±0.74%, 9.06±1.99% and 10.10±0.17% re- spectively. Protein content for the gelatin extracted at temperature 60°C, 70°C and 80°C were 26.61±0.82%, 28.04±1.07% and 33.00±0.35% respectively. Moisture, lipid and ash content for three type of gelatin extracted at tempera- ture 60°C, 70°C and 80°C had significant different (p 0.05). Color determi- nation and gel strength of gelatin were show the significant different (p<0.05). Value: Thus, gel strength of gelatin extracted inversely proportional to the ex- traction temperature.
Epidemiology of Zygomycosis: Analysis of National Data from Pathological Autopsy Cases in Japan.

BACKGROUND AND METHODS To identify recent trends in the frequency of zygomycosis in autopsy cases, we conducted epidemiological analysis every four years from 1989 to 2009 using national data reported in the "Annual of Pathological Autopsy Cases in Japan. " RESULTS 153,615 cases were autopsied, of which 6622 (4.3%) were found to have had mycosis. Among these, there were 243 cases (3.7%) of zygomycosis, which was the fourth most predominant causative agent of mycoses among the monopathogen mycoses. Of the complicated mycoses, zygomycosis accounted for 56 cases. A total of 299 cases with zygomycoses were observed. The frequency of zygomycosis appeared to be generally stable over the twenty-year period from 1989 to 2009, at around 4% of autopsy cases having mycosis. Younger patients tended to have severe and complicated infections that were characteristic of zygomycosis, compared with non-zygomycosis. The pulmonary and gastrointestinal (GI) systems were the most common foci in our analysis, reflecting the severity of zygomycosis in these sites. Hematological disease was the most frequent underlying disease, but there was a peak of neonatal infections in 2009, which was the first time that this was observed in our studies. CONCLUSION These results of the epidemiological analysis of autopsy cases with mycosis demonstrate that clinicians should promptly recognize and treat zygomycosis.
LONG-TERM IMPLANTATION OF PRIMARY ISLET CELL-ENCAPSULATING HYDROGEL MICROFIBERS IN DIABETIC MICE

This paper describes long-term implantation of primary pancreatic islet cell fibers into diabetic mice. Primary rat pancreatic islet cells were encapsulated in core-shell hydrogel microfibers and implanted into renal capsular space of diabetic mice by using a microcatheter. The blood glucose concentration of the recipient mice were normalized for more than 36 days. This result shows that our cell fiber approach can be applied to long-term implantation and can provide primary islet cells with sufficient microenvironment to promote cellular functions in vivo.
Combined cistrome and transcriptome analysis of SKI in AML cells identifies SKI as a co-repressor for RUNX1

Abstract SKI is a transcriptional co-regulator and overexpressed in various human tumors, for example in acute myeloid leukemia (AML). SKI contributes to the origin and maintenance of the leukemic phenotype. Here, we use ChIP-seq and RNA-seq analysis to identify the epigenetic alterations induced by SKI overexpression in AML cells. We show that approximately two thirds of differentially expressed genes are up-regulated upon SKI deletion, of which >40% harbor SKI binding sites in their proximity, primarily in enhancer regions. Gene ontology analysis reveals that many of the differentially expressed genes are annotated to hematopoietic cell differentiation and inflammatory response, corroborating our finding that SKI contributes to a myeloid differentiation block in HL60 cells. We find that SKI peaks are enriched for RUNX1 consensus motifs, particularly in up-regulated SKI targets upon SKI deletion. RUNX1 ChIP-seq displays that nearly 70% of RUNX1 binding sites overlap with SKI peaks, mainly at enhancer regions. SKI and RUNX1 occupy the same genomic sites and cooperate in gene silencing. Our work demonstrates for the first time the predominant co-repressive function of SKI in AML cells on a genome-wide scale and uncovers the transcription factor RUNX1 as an important mediator of SKI-dependent transcriptional repression.
Mean–Variance Analysis for the Newsvendor Problem

The newsvendor problem is a fundamental building block for inventory management with a stochastic demand. The classical newsvendor problem focuses on a sole objective of either minimizing the expected cost or maximizing the expected profit. However, the performance measure with expected value alone is insufficient, and it ignores the risk preferences of the decision makers. As a result, we carry out a mean-variance analysis of the newsvendor problem. We construct analytical models and reveal the problem's structural properties. We propose the solution schemes which help to identify the optimal solutions. Interesting findings regarding the efficient frontier, the case with a stockout penalty cost, and the safety-first objective are discussed.
Depression Anxiety Stress Scales (DASS-21): Factor Structure in Traumatic Brain Injury Rehabilitation

Objective: To confirm the construct validity of the Depression Anxiety Stress Scales-21 (DASS-21) by investigating the fit of published factor structures in a sample of adults with moderate to severe traumatic brain injury (posttraumatic amnesia > 24 hours). Participants: Archival data from 504 patient records at the Brain Injury Rehabilitation Unit at Liverpool Hospital, Australia. Participants were aged between 16 and 71 years and were engaged in a specialist rehabilitation program. Main Measure: The DASS-21. Results: Two of the 6 models had adequate fit using structural equation modeling. The data best fit Henry and Crawford's quadripartite model, which comprised a Depression, Anxiety and Stress factor, as well as a General Distress factor. The data also adequately fit Lovibond and Lovibond's original 3-factor model, and the internal consistencies of each factor were very good (&agr; = 0.82–0.90). Conclusion: This study confirms the structure and construct validity of the DASS-21 and provides support for its use as a screening tool in traumatic brain injury rehabilitation.
More Polarized but More Independent

In three nationally representative surveys of U.S. residents (N = 10 million) from 1970 to 2015, more Americans in the early 2010s (vs. previous decades) identified as Independent, including when age effects were controlled. More in the early 2010s (vs. previous decades) expressed polarized political views, including stronger political party affiliation or more extreme ideological self-categorization (liberal vs. conservative) with fewer identifying as moderate. The correlation between party affiliation and ideological views grew stronger over time. The overall trend since the 1970s was toward more Americans identifying as Republican or conservative. Older adults were more likely to identify as conservative and Republican. More Millennials (born 1980-1994) identify as conservative than either GenXers or Boomers did at the same age, and fewer are Democrats compared with Boomers. These trends are discussed in the context of social identification processes and their implications for the political dynamics in the United States.
Reinforced Concrete response to simulated earthquakes

A series of reinforced concrete specimens has been subjected to static tests as well as periodic and simulated earthquake motions to develop realistic analytical models for the earthquake response of the elements and materials involved. During some of the dynamic tests the specimen responded with a displacement of the order of six times the initial yield deflection. The stiffness and energy absorbing capacity of the specimens changed considerably and, at times, very rapidly during the dynamic tests. A realistic conceptual model for predicting the dynamic response of a reinforced concrete member should be based on a static force-displacement relationship which reflects the changes in stiffness for loading and unloading as a function of the previous loading history. The dynamic response calculated on the basis of the proposed force-displacement relationship resulted in satisfactory agreement with the measured response. With the hysteresis loops defined by the proposed force-displacement relationship, it was not necessary to invoke additional sources of energy absorption for a satisfactory prediction of the dynamic response.
THE EFFECTS OF POLYMER TYPE AND RATIO ON THE EXTENDED RELEASE OF ATENOLOL FROM HYDROPHILIC MATRICES

In this study, the effects of type and ratio of the polymers [hydroxypropylmethylcellulose (Methocel ® K100LV and K15M), methacrylic acid copolymer (Eudragit ® L100)] and direct compression agents (Pharmatose DCL11 ® , Cellactose ® 80, Microcel ® PH101) on the extended release of atenolol from hydrophilic matrix tablets prepared by direct compression method were investigated. Spectrophotometric method used for the determination of atenolol in dissolution media was validated by calculating linearity and range, precision, accuracy and specificity values. The dissolution profiles showed that hydroxypropylmethylcellulose ratio and type play a significant role in drug release and direct compression agents (lactose or cellulose based) can be effective on drug release at the presence of low amounts of hydroxypropylmethylcellulose in the formulations. It is also observed that methacrylic acid copolymer could not effectively hinder the drug release in acidic medium and binary mixtures of polymers could lead to discontinuous drug release profiles. Results indicated that low viscosity grade hydroxypropylmethylcellulose can be preferred to obtain linear drug release profiles for a duration of eight hours with a lactose-based direct compression agent. Results of kinetic data indicated that atenolol release from the formulations generally fits best to the Korsmeyer-Peppas kinetic model and drug release mechanism shows non-Fickian transport mechanism according to the values of diffusion exponent.
A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data

Motivation: Gene-expression data obtained from high throughput technologies are subject to various sources of noise and accordingly the raw data are pre-processed before formally analyzed. Normalization of the data is a key pre-processing step, since it removes systematic variations across arrays. There are numerous normalization methods available in the literature. Based on our experience, in the context of oscillatory systems, such as cell-cycle, circadian clock, etc., the choice of the normalization method may substantially impact the determination of a gene to be rhythmic. Thus rhythmicity of a gene can purely be an artifact of how the data were normalized. Since the determination of rhythmic genes is an important component of modern toxicological and pharmacological studies, it is important to determine truly rhythmic genes that are robust to the choice of a normalization method. Results: In this paper we introduce a rhythmicity measure and a bootstrap methodology to detect rhythmic genes in an oscillatory system. Although the proposed methodology can be used for any high-throughput gene expression data, in this paper we illustrate the proposed methodology using several publicly available circadian clock microarray gene-expression datasets. We demonstrate that the choice of normalization method has very little effect on the proposed methodology. Specifically, for any pair of normalization methods considered in this paper, the resulting values of the rhythmicity measure are highly correlated. Thus it suggests that the proposed measure is robust to the choice of a normalization method. Consequently, the rhythmicity of a gene is potentially not a mere artifact of the normalization method used. Lastly, as demonstrated in the paper, the proposed bootstrap methodology can also be used for simulating data for genes participating in an oscillatory system using a reference dataset. Availability: A user friendly code implemented in R language can be downloaded from http://www.eio. uva.es/~miguel/robustdetectionprocedure.html
Mismatch repair deficiency may be common in ductal adenocarcinoma of the prostate

Precision oncology entails making treatment decisions based on a tumor's molecular characteristics. For prostate cancer, identifying clinically relevant molecular subgroups is challenging, as molecular profiling is not routine outside of academic centers. Since histologic variants of other cancers correlates with specific genomic alterations, we sought to determine if ductal adenocarcinoma of the prostate (dPC) – a rare and aggressive histopathologic variant – was associated with any recurrent actionable mutations. Tumors from 10 consecutive patients with known dPC were sequenced on a targeted next-generation DNA sequencing panel. The median age at diagnosis was 59 years (range, 40–73). Four (40%) patients had metastases upon presentation. Archival tissue from formalin-fixed paraffin-embedded prostate tissue samples from nine patients and a biopsy of a metastasis from one patient with castration-resistant prostate cancer were available for analysis. Nine of 10 samples had sufficient material for tumor sequencing. Four (40%) patients' tumors had a mismatch repair (MMR) gene alteration (N = 2, MSH2; N = 1, MSH6; and N = 1, MLH1), of which 3 (75%) had evidence of hypermutation. Sections of the primary carcinomas of three additional patients with known MMR gene alterations/hypermutation were histologically evaluated; two of these tumors had dPC. MMR mutations associated with hypermutation were common in our cohort of dPC patients. Since hypermutation may predict for response to immune checkpoint blockade, the presence of dPC may be a rapid means to enrich populations for further screening. Given our small sample size, these findings require replication.
Race, disability, and grade: Social relationships in children with autism spectrum disorders

Race is associated with social relationships among typically developing children; however, studies rarely examine the impact of race on social outcomes for children with autism spectrum disorder. This study examined how race (African American, Latino, Asian, or White) in conjunction with disability status (autism spectrum disorders or typically developing) and grade (grades K–2 or 3–5) affects friendships and social networks. The sample comprises 85 children with autism spectrum disorders and 85 typically developing controls matched on race, gender, age/grade, and classroom (wherever possible). Race, disability, and grade each had an independent effect on friendship nominations, and there was an interaction among the three variables. Specifically, children with autism spectrum disorders who were African American or Latino in the upper elementary grades received fewer friendship nominations than typically developing White children in the lower elementary grades. Only the presence of autism spectrum disorders was associated with social network centrality. Our results also suggested that Latino children with autism spectrum disorders in the upper elementary grades were at the highest risk of social isolation. Implications for re-conceptualizing social skills interventions are discussed.
Review of differentiated approaches to antiretroviral therapy distribution

ABSTRACT In response to global trends of maximizing the number of patients receiving antiretroviral therapy (ART), this review summarizes literature describing differentiated models of ART distribution at facility and community levels in order to highlight promising strategies and identify evidence gaps. Databases and gray literature were searched, yielding thirteen final articles on differentiated ART distribution models supporting stable adult patients. Of these, seven articles focused on distribution at facility level and six at community level. Findings suggest that differentiated models of ART distribution contribute to higher retention, lower attrition, and less loss to follow-up (LTFU). These models also reduced patient wait time, travel costs, and time lost from work for drug pick-up. Facility- and community-level ART distribution models have the potential to extend treatment availability, enable improved access and adherence among people living with HIV (PLHIV), and facilitate retention in treatment and care. Gaps remain in understanding the desirability of these models for PLHIV, and the need for more information the negative and positive impacts of stigma, and identifying models to reach traditionally marginalized groups such as key populations and youth. Replicating differentiated care so efforts can reach more PLHIV will be critical to scaling these approaches across varying contexts.
Accuracy of molecular biology techniques for the diagnosis of Strongyloides stercoralis infection—A systematic review and meta-analysis

Background Strongyloides stercoralis infection is a neglected tropical disease which can lead to severe symptoms and even death in immunosuppressed people. Unfortunately, its diagnosis is hampered by the lack of a gold standard, as the sensitivity of traditional parasitological tests (including microscopic examination of stool samples and coproculture) is low. Hence, alternative diagnostic methods, such as molecular biology techniques (mostly polymerase chain reaction, PCR) have been implemented. However, there are discrepancies in the reported accuracy of PCR. Methodology A systematic review with meta-analysis was conducted in order to evaluate the accuracy of PCR for the diagnosis of S. stercoralis infection. The protocol was registered with PROSPERO International Prospective Register of Systematic Reviews (record: CRD42016054298). Fourteen studies, 12 of which evaluating real-time PCR, were included in the analysis. The specificity of the techniques resulted high (ranging from 93 to 95%, according to the reference test(s) used). When all molecular techniques were compared to parasitological methods, the sensitivity of PCR was assessed at 71.8% (95% CI 52.2–85.5), that decreased to 61.8% (95% CI 42.0–78.4) when serology was added among the reference tests. Similarly, sensitivity of real-time PCR resulted 64.4% (95% CI 46.2–77.7) when compared to parasitological methods only, 56.5% (95% CI 39.2–72.4) including serology. Conclusions PCR might not be suitable for screening purpose, whereas it might have a role as a confirmatory test.
Summer heat: a cross-sectional analysis of seasonal differences in sexual behaviour and sexually transmissible diseases in Melbourne, Australia

Objectives To date, no study has correlated seasonal differences in sexual behaviour with the seasonal differences in sexually transmitted infections (STIs); and no seasonal study of STIs has been conducted in the southern hemisphere. Our study aimed to describe seasonal differences in sexual behaviour and correlate this with seasonal differences in STI diagnoses in Melbourne, Australia. Method This was a cross-sectional study of individuals attending the Melbourne Sexual Health Centre over a 9-year period from 2006 to 2014. We conducted separate analyses for men who have sex with men (MSM) and men who have sex with women (MSW), and women. Seasonal patterns of sexual behaviour and STI positivity were examined within each group. Results All groups reported a higher number of partners over the preceding three months for consultations in summer compared with winter (MSM mean 5.48 vs 5.03; MSW mean 2.46 vs 2.31; women mean 1.83 vs 1.72). Urethral gonorrhoea diagnoses among MSM were higher in summer compared with winter (OR 1.23, 95% CI 1.04 to 1.46). Similarly, non-gonococcal urethritis (NGU) diagnoses among MSW were the highest in summer (OR 1.11, 95% CI 1.03 to 1.20), but there was no seasonal difference in NGU diagnoses when we adjusted for partner numbers. In women, pelvic inflammatory disease (PID) diagnoses peaked in autumn, when rates were higher than in winter (OR 1.30, 95% CI 1.09 to 1.55). Conclusions Our results describe a peak in sexual partner number and STI diagnoses during consultations in summer in men and a rise in PID in autumn in women.
Error Correction and Degeneracy in Surface Codes Suffering Loss

Many proposals for quantum information processing are subject to detectable loss errors. In this paper, we give a detailed account of recent results in which we showed that topological quantum memories can simultaneously tolerate both loss errors and computational errors, with a graceful tradeoff between the threshold for each. We further discuss a number of subtleties that arise when implementing error correction on topological memories. We particularly focus on the role played by degeneracy in the matching algorithms and present a systematic study of its effects on thresholds. We also discuss some of the implications of degeneracy for estimating phase transition temperatures in the random bond Ising model.