Miracle-dz/UniFAR-FTUs huggingface dataset:
Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.
Fine Characterisation of a Recombination Hotspot at the DPY19L2 Locus and Resolution of the Paradoxical Excess of Duplications over Deletions in the General Population

We demonstrated previously that 75% of infertile men with round, acrosomeless spermatozoa (globozoospermia) had a homozygous 200-Kb deletion removing the totality of DPY19L2. We showed that this deletion occurred by Non-Allelic Homologous Recombination (NAHR) between two homologous 28-Kb Low Copy Repeats (LCRs) located on each side of the gene. The accepted NAHR model predicts that inter-chromatid and inter-chromosome NAHR create a deleted and a duplicated recombined allele, while intra-chromatid events only generate deletions. Therefore more deletions are expected to be produced de novo. Surprisingly, array CGH data show that, in the general population, DPY19L2 duplicated alleles are approximately three times as frequent as deleted alleles. In order to shed light on this paradox, we developed a sperm-based assay to measure the de novo rates of deletions and duplications at this locus. As predicted by the NAHR model, we identified an excess of de novo deletions over duplications. We calculated that the excess of de novo deletion was compensated by evolutionary loss, whereas duplications, not subjected to selection, increased gradually. Purifying selection against sterile, homozygous deleted men may be sufficient for this compensation, but heterozygously deleted men might also suffer a small fitness penalty. The recombined alleles were sequenced to pinpoint the localisation of the breakpoints. We analysed a total of 15 homozygous deleted patients and 17 heterozygous individuals carrying either a deletion (n = 4) or a duplication (n = 13). All but two alleles fell within a 1.2-Kb region central to the 28-Kb LCR, indicating that >90% of the NAHR took place in that region. We showed that a PRDM9 13-mer recognition sequence is located right in the centre of that region. Our results therefore strengthen the link between this consensus sequence and the occurrence of NAHR.
PENGARUH KOMPETENSI, INDEPENDENSI DAN ETIKA PROFESI AUDITOR TERHADAP KUALITAS AUDIT (STUDI EMPIRIS PADA KAP DI MALANG)

This study aims to analyze the effect of competence, independence, and auditor’s professional ethic toward audit quality in public accountant firm located in Malang. The finding of this research suggested that competence and independence did not significantly influence the audit quality, while the auditor’s professional ethic had a significant influence on it. Keywords: competence, independence,auditor’s professional ethic, audit quality
HOMOMORPHISMS AND DERIVATIONS ON UNITAL C ∗ − ALGEBRAS RELATED TO CAUCHY – JENSEN FUNCTIONAL INEQUALITY

In this paper, we investigate homomorphisms from unital C∗−algebras to unital Banach algebras and derivations from unital C∗−algebras to Banach A−modules related to a Cauchy–Jensen functional inequality. Mathematics subject classification (2010): 39B72, 46H30, 46B06.
Incidence of End-Stage Renal Disease in the Turkish-Cypriot Population of Northern Cyprus: A Population Based Study

Background This is the first report of the incidence and causes of end-stage renal disease (ESRD) of the Turkish-Cypriot population in Northern Cyprus. Methods Data were collected over eight consecutive years (2004–2011) from all those starting renal replacement therapy (RRT) in this population. Crude and age-standardised incidence at 90 days was calculated and comparisons made with other national registries. We collected DNA from the entire prevalent population. As an initial experiment we looked for two genetic causes of ESRD that have been reported in Greek Cypriots. Results Crude and age-standardised incidence at 90 days was 234 and 327 per million population (pmp) per year, respectively. The mean age was 63, and 62% were male. The age-adjusted prevalence of RRT in Turkish-Cypriots was 1543 pmp on 01/01/2011. The incidence of RRT is higher than other countries reporting to the European Renal Association – European Dialysis and Transplant Association, with the exception of Turkey. Diabetes is a major cause of ESRD in those under 65, accounting for 36% of incident cases followed by 30% with uncertain aetiology. 18% of the incident population had a family history of ESRD. We identified two families with thin basement membrane nephropathy caused by a mutation in COL4A3, but no new cases of CFHR5 nephropathy. Conclusions This study provides the first estimate of RRT incidence in the Turkish-Cypriot population, describes the contribution of different underlying diagnoses to ESRD, and provides a basis for healthcare policy planning.
Performance of histogram descriptors for the classification of 3D laser range data in urban environments

The selection of suitable features and their parameters for the classification of three-dimensional laser range data is a crucial issue for high-quality results. In this paper we compare the performance of different histogram descriptors and their parameters on three urban datasets recorded with various sensors-sweeping SICK lasers, tilting SICK lasers and a Velodyne 3D laser range scanner. These descriptors are 1D, 2D, and 3D histograms capturing the distribution of normals or points around a query point. We also propose a novel histogram descriptor, which relies on the spectral values in different scales. We argue that choosing a larger support radius and a z-axis based global reference frame/axis can boost the performance of all kinds of investigated classification models significantly. The 3D histograms relying on the point distribution, normal orientations, or spectral values, turned out to be the best choice for the classification in urban environments.
Measurements of Piezoelectric Coefficient d33 of Lead Zirconate Titanate Thin Films Using a Mini Force Hammer

Lead zirconate titanate (PbZrxTi1-xO3, or PZT) is a piezoelectric material widely used as sensors and actuators. For microactuators, PZT often appears in the form of thin films to maintain proper aspect ratios. One major challenge encountered is accurate measurement of piezoelectric coefficients of PZT thin films. In this paper, we present a simple, low-cost, and effective method to measure piezoelectric coefficient d33 of PZT thin films through use of basic principles in mechanics of vibration. A small impact hammer with a tiny tip acts perpendicularly to the PZT thin-film surface to generate an impulsive force. In the meantime, a load cell at the hammer tip measures the impulsive force and a charge amplifier measures the responding charge of the PZT thin film. Then the piezoelectric coefficient d33 is obtained from the measured force and charge based on piezoelectricity and a finite element modeling. We also conduct a thorough parametric study to understand the sensitivity of this method on various parameters, such as substrate material, boundary conditions, specimen size, specimen thickness, thickness ratio, and PZT thin-film material. Two rounds of experiments are conducted to demonstrate the feasibility and accuracy of this new method. The first experiment is to measure d33 of a PZT disk resonator whose d33 is known. Experimental results show that d33 measured via this method is as accurate as that from the manufacturer's specifications within its tolerance. The second experiment is to measure d33 of PZT thin films deposited on silicon substrates. With the measured d33, we predict the displacement of PZT thin-film membrane microactuators. In the meantime, the actuator displacement is measured via a laser Doppler vibrometer. The predicted and measured displacements agree very well validating the accuracy of this new method.
ARBITRAGE, HEDGING, SPECULATION AND THE PRICING OF CRUDE OIL FUTURES CONTRACTS

A model is presented to explain the determination of commodity futures prices in terms of the activities of arbitrageurs and speculators. The model is tested for various maturities using the WTI crude oil as a representative commodity. The results show that the futures price is determined by the activities of arbitrageurs and futures (not spot) speculators. JEL Classification Number: C12, C51, G12
apt-p2p: A Peer-to-Peer Distribution System for Software Package Releases and Updates

The Internet has become a cost-effective vehicle for software development and release, particular in the free software community. Given the free nature of this software, there are often a number of users motivated by altruism to help out with the distribution, so as to promote the healthy development of this voluntary society. It is thus naturally expected that a peer-to- peer distribution can be implemented, which will scale well with large user bases, and can easily explore the network resources made available by the volunteers. Unfortunately, this application scenario has many unique characteristics, which make a straightforward adoption of existing peer-to-peer systems for file sharing (such as BitTorrent) suboptimal. In particular, a software release often consists of a large number of packages, which are difficult to distribute individually, but the archive is too large to be distributed in its entirety. The packages are also being constantly updated by the loosely-managed developers, and the interest in a particular version of a package can be very limited depending on the computer platforms and operating systems used. In this paper, we propose a novel peer-to-peer assisted distribution system design that addresses the above challenges. It enhances the existing distribution systems by providing compatible and yet more efficient downloading and updating services for software packages. Our design leads to apt-p2p, a practical implementation that extends the popular apt distributor. apt-p2p has been used in conjunction with Debian-based distribution of Linux software packages and is also available in the latest release of Ubuntu. We have addressed the key design issues in apt-p2p, including indexing table customization, response time reduction, and multi-value extension. They together ensure that the altruistic users' resources are effectively utilized and thus significantly reduces the currently large bandwidth requirements of hosting the software, as confirme- d by our existing real user statistics gathered over the Internet.
Clinical presentations of X-linked retinoschisis in Taiwanese patients confirmed with genetic sequencing

Purpose To investigate the clinical characteristics of X-linked retinoschisis (XLRS) and identify genetic mutations in Taiwanese patients with XLRS. Methods This study included 23 affected males from 16 families with XLRS. Fundus photography, spectral domain optical coherent tomography (SD-OCT), fundus autofluorescence (FAF), and full-field electroretinograms (ERGs) were performed. The coding regions of the RS1 gene that encodes retinoschisin were sequenced. Results The median age at diagnosis was 18 years (range 4–58 years). The best-corrected visual acuity ranged from no light perception to 20/25. The typical spoke-wheel pattern in the macula was present in 61% of the patients (14/23) while peripheral retinoschisis was present in 43% of the patients (10/23). Four eyes presented with vitreous hemorrhage, and two eyes presented with leukocoria that mimics Coats’ disease. Macular schisis was identified with SD-OCT in 82% of the eyes (31/38) while foveal atrophy was present in 18% of the eyes (7/38). Concentric area of high intensity was the most common FAF abnormality observed. Seven out of 12 patients (58%) showed electronegative ERG findings. Sequencing of the RS1 gene identified nine mutations, six of which were novel. The mutations are all located in exons 4–6, including six missense mutations, two nonsense mutations, and one deletion-caused frameshift mutation. Conclusions XLRS is a clinically heterogeneous disease with profound phenotypic inter- and intrafamiliar variability. Genetic sequencing is valuable as it allows a definite diagnosis of XLRS to be made without the classical clinical features and ERG findings. This study showed the variety of clinical features of XLRS and reported novel mutations.
Improved specificity of gene silencing by siRNAs containing unlocked nucleobase analogs

siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that unlocked nucleobase analogs (UNAs) confer desirable properties to siRNAs. Addition of a single UNA at the 5′-terminus of the passenger strand blocks participation of the passenger strand in RISC-mediated target down-regulation with a concomitant increase in guide strand activity. Placement of a UNA in the seed region of the guide strand prevents miRNA-like off-target silencing without compromising siRNA activity. Most significantly, combined substitution of UNA at the 3′-termini of both strands, the addition of a UNA at the 5′-terminus of the passenger strand, and a single UNA in the seed region of the guide strand, reduced the global off-target events by more than 10-fold compared to unmodified siRNA. The reduction in off-target events was specific to UNA placement in the siRNA, with no apparent new off-target events. Taken together, these results indicate that when strategically placed, UNA substitutions have important implications for the design of safe and effective siRNA-based therapeutics.
Human Impacts and Climate Change Influence Nestedness and Modularity in Food-Web and Mutualistic Networks

Theoretical studies have indicated that nestedness and modularity—non-random structural patterns of ecological networks—influence the stability of ecosystems against perturbations; as such, climate change and human activity, as well as other sources of environmental perturbations, affect the nestedness and modularity of ecological networks. However, the effects of climate change and human activities on ecological networks are poorly understood. Here, we used a spatial analysis approach to examine the effects of climate change and human activities on the structural patterns of food webs and mutualistic networks, and found that ecological network structure is globally affected by climate change and human impacts, in addition to current climate. In pollination networks, for instance, nestedness increased and modularity decreased in response to increased human impacts. Modularity in seed-dispersal networks decreased with temperature change (i.e., warming), whereas food web nestedness increased and modularity declined in response to global warming. Although our findings are preliminary owing to data-analysis limitations, they enhance our understanding of the effects of environmental change on ecological communities.
Version of December 30 , 2002 Inheritance and Charitable Donations

In this paper, we employ a unique new data set (the Philanthropy Panel Study (PPS), a module within the Panel Study of Income Dynamics (PSID)) to test whether the propensity to donate out of inherited wealth is equal to the propensities to donate out of other wealth, earned income, and transfer payments. We find that the elasticity of giving from non-inherited wealth is much greater than from inherited wealth for total giving and gifts to religion, combined causes, people in need, health, education, and other causes. The effects of income derived from inherited wealth and labor income are similar in terms of elasticities, although inherited wealth creates a higher marginal propensity to donate. Transfer income has either a small or no apparent effect on donations.
Assessing Granger Causality in Electrophysiological Data: Removing the Adverse Effects of Common Signals via Bipolar Derivations

Multielectrode voltage data are usually recorded against a common reference. Such data are frequently used without further treatment to assess patterns of functional connectivity between neuronal populations and between brain areas. It is important to note from the outset that such an approach is valid only when the reference electrode is nearly electrically silent. In practice, however, the reference electrode is generally not electrically silent, thereby adding a common signal to the recorded data. Volume conduction further complicates the problem. In this study we demonstrate the adverse effects of common signals on the estimation of Granger causality, which is a statistical measure used to infer synaptic transmission and information flow in neural circuits from multielectrode data. We further test the hypothesis that the problem can be overcome by utilizing bipolar derivations where the difference between two nearby electrodes is taken and treated as a representation of local neural activity. Simulated data generated by a neuronal network model where the connectivity pattern is known were considered first. This was followed by analyzing data from three experimental preparations where a priori predictions regarding the patterns of causal interactions can be made: (1) laminar recordings from the hippocampus of an anesthetized rat during theta rhythm, (2) laminar recordings from V4 of an awake-behaving macaque monkey during alpha rhythm, and (3) ECoG recordings from electrode arrays implanted in the middle temporal lobe and prefrontal cortex of an epilepsy patient during fixation. For both simulation and experimental analysis the results show that bipolar derivations yield the expected connectivity patterns whereas the untreated data (referred to as unipolar signals) do not. In addition, current source density signals, where applicable, yield results that are close to the expected connectivity patterns, whereas the commonly practiced average re-reference method leads to erroneous results.
This Article Has Been Accepted for Publication in a Future Issue of Ieee Trans. Fuzzy Sys., but Has Not Been Fully Edited. Content May Change Prior to Final Publication. Scene Image Is Non-mutually Exclusive - a Fuzzy Qualitative Scene Understanding

—Ambiguity or uncertainty is a pervasive element of many real world decision making processes. Variation in decisions is a norm in this situation when the same problem is posed to different subjects. Psychological and metaphysical research had proven that decision making by human is subjective. It is influenced by many factors such as experience, age, background, etc. Scene understanding is one of the computer vision problems that fall into this category. Conventional methods relax this problem by assuming scene images are mutually exclusive; and therefore, focus on developing different approaches to perform the binary classification tasks. In this paper, we show that scene images are non-mutually exclusive, and propose the Fuzzy Qualitative Rank Classifier (FQRC) to tackle the aforementioned problems. The proposed FQRC provides a ranking interpretation instead of binary decision. Evaluations in term of qualitative and quantitative using large numbers and challenging public scene datasets have shown the effectiveness of our proposed method in modeling the non-mutually exclusive scene images.
Human Brain Representation of Pleasant and Aversive Taste in the

[PDF] [Full Text] [Abstract] , November 23, 2010; 107 (47): 20529-20534. PNAS Seeley, Stephen C. Woods and James P. Herman Davis, Matia B. Solomon, Annette D. de Kloet, Kellie L. Tamashiro, Randall R. Sakai, Randy J. Kenneth R. Jones, Dennis C. Choi, Eric G. Krause, Nathan K. Evanson, Amy R. Furay, Jon F. Yvonne M. Ulrich-Lai, Anne M. Christiansen, Michelle M. Ostrander, Amanda A. Jones, Pleasurable behaviors reduce stress via brain reward pathways [PDF] [Full Text] [Abstract] , January 4, 2011; 108 (1): 55-60. PNAS Jian Li, Mauricio R. Delgado and Elizabeth A. Phelps How instructed knowledge modulates the neural systems of reward learning [PDF] [Full Text] [Abstract] , March , 2011; 6 (2): 114-133. Perspectives on Psychological Science Mara Mather and Matthew R. Sutherland Arousal-Biased Competition in Perception and Memory [PDF] [Full Text] [Abstract] , March 23, 2011; 31 (12): 4360-4366. J. Neurosci. Eric Stice, Sonja Yokum, Kyle S. Burger, Leonard H. Epstein and Dana M. Small to Food Youth at Risk for Obesity Show Greater Activation of Striatal and Somatosensory Regions
Lifestyle, nutrition and breast cancer: facts and presumptions for consideration

Breast cancer is the most common cancer in women worldwide, and the high incidence of this cancer coupled with improvements in initial treatments has led to an ever-increasing number of breast cancer survivors. Among the prospective epidemiological studies on diet and breast cancer incidence and recurrence, to date, there is no association that is strong, reproducible and statistically significant, with the exception of alcohol intake, overweight, and weight gain. Nevertheless, many beliefs about food and breast cancer persist in the absence of supporting scientific evidence. After a comprehensive review regarding the role of lifestyle on breast cancer outcomes and a thorough study of the dissemination field including mass media, clinical institutions, and academic figures, we briefly reported the most common presumptions and also facts from the literature regarding lifestyle, nutrition, and breast cancer. The randomised controlled trial is the best study-design that could provide direct evidence of a causal relationship; however, there are methodological difficulties in applying and maintaining a lifestyle intervention for a sufficient period; consequently, there is a lack of this type of study in the literature. Instead, it is possible to obtain indirect evidence from observational prospective studies. In this article, it becomes clear that for now the best advice for women’s health is to follow the World Cancer Research Fund/American Institute of Cancer Research (WCRF/AICR) recommendations on diet, nutrition, physical activity, and weight management for cancer prevention, because they are associated with a lower risk of developing most types of cancer, including breast cancer. Despite current awareness of the role of nutrition in cancer outcomes, there is inadequate translation from research findings into clinical practice. We suggest the establishment of a multidisciplinary research consortium to demonstrate the real power of lifestyle interventions.