Miracle-dz/UniFAR-FTUs huggingface dataset:
Whole Exome Sequencing of Rapid Autopsy Tumors and Xenograft Models Reveals Possible Driver Mutations Underlying Tumor Progression

Pancreatic Ductal Adenocarcinoma (PDAC) is a highly lethal malignancy due to its propensity to invade and rapidly metastasize and remains very difficult to manage clinically. One major hindrance towards a better understanding of PDAC is the lack of molecular data sets and models representative of end stage disease. Moreover, it remains unclear how molecularly similar patient-derived xenograft (PDX) models are to the primary tumor from which they were derived. To identify potential molecular drivers in metastatic pancreatic cancer progression, we obtained matched primary tumor, metastases and normal (peripheral blood) samples under a rapid autopsy program and performed whole exome sequencing (WES) on tumor as well as normal samples. PDX models were also generated, sequenced and compared to tumors. Across the matched data sets generated for three patients, there were on average approximately 160 single-nucleotide mutations in each sample. The majority of mutations in each patient were shared among the primary and metastatic samples and, importantly, were largely retained in the xenograft models. Based on the mutation prevalence in the primary and metastatic sites, we proposed possible clonal evolution patterns marked by functional mutations affecting cancer genes such as KRAS, TP53 and SMAD4 that may play an important role in tumor initiation, progression and metastasis. These results add to our understanding of pancreatic tumor biology, and demonstrate that PDX models derived from advanced or end-stage likely closely approximate the genetics of the disease in the clinic and thus represent a biologically and clinically relevant pre-clinical platform that may enable the development of effective targeted therapies for PDAC.
Multitasking : the Uncertain Impact of Technology on Knowledge Workers and Managers

While the productivity paradox has now been officially pronounced dead, the argument and the evidence for this assertion are both at a macroeconomic level. What has been less closely examined is the microeconomic impact of recent developments in ICT on the productivity of office and knowledge workers. There is an assumption, readily seen in many advertisements for mobile technology, that multi-tasking, WiFi connected laptops, Blackberrys, smart phones and so on are good for business and make people more effective and productive. This may be true some of the time and there is some (albeit limited) research which supports claims that these technologies increase productivity. However there are also emerging concerns that, in certain environments, these technologies may actually reduce productivity in both the short and the long term. This paper examines this problem and research to date and proposes a framework for further investigation of this phenomenon.
Office Appliance Classification From Disaggregated Plug-Load Data

As buildings consume 40% of US primary energy, energy efficiency through smart plug-load management can have a significant impact on US carbon emissions. In this paper we investigate learning algorithms to classify plug-loads based on minutely energy plug-load data and hourly weather data. One month of data is preprocessed into 31 daily features which are used to classify 5660 training samples into 31 labels using a range of multi-class classification algorithms. Of all models tested, random forest trees performed the best, with a test error of 17%. This promising result can likely be further refined with improved feature selection, and a larger dataset. Future work will focus on increasing the model performance and integrating it into a useful product for plug-load management companies.
The Blue Studio: Designing an Interactive Environment for Embodied Multi-Stakeholder Ideation Processes

This paper describes the process of designing the Blue Studio: an interactive space for embodied multi-stakeholder ideation processes. Inspired by embodied sensemaking -- the way people make sense of things through external expression and interaction with other people -- we iteratively designed material, interactive and spatial interventions in the Blue Studio and evaluated them with multi-stakeholder participants in various studies. Thereupon, we analyzed the impact of the design interventions, based on the seven principles to design for embodied sensemaking and highlighted opportunities for refining our interactive space for embodied ideation. Based on the insights gained, a final design of the Blue Studio was realized and evaluated on functionality.
Spontaneous Rupture of an Unscarred Gravid Uterus in a Primigravid Woman at 32 Weeks of Gestation

Uterine rupture usually occurs in a scarred uterus, especially secondary to prior cesarean section. Antepartum uterine rupture in an unscarred uterus is extremely rare. We report a case of spontaneous rupture of an unscarred gravid uterus at 32 weeks of gestation in a primigravid woman. Ultrasonography and magnetic resonance imaging showed a bulging cystic lesion communicating with the intrauterine cavity. Operative findings during emergent cesarean section revealed uterine perforation in the right cornual area and a prolapsed, nonbleeding amniotic sac. The left cornual area was also focally thin. An arcuate uterus was suspected based on follow-up hysterosalpingography. Antepartum uterine rupture tends to occur in the uterine cornual area. In this case, Müllerian duct anomalies may have been associated with focal myometrial defects.
Reconstructing evolutionary modular networks from time series data

The behavior and dynamics of complex systems are in focus of many research fields. The complexity of such systems comes not only from the number of their elements but also from the unavoidable emergence of new properties of the system, which are not just a simple summation of the properties of its elements. The behavior of complex systems can be fitted with a number of well developed models, which, however, do not incorporate the modularity and the evolution of a system simultaneously. In this paper, we propose a generalized model that addresses this issue. In our model, the random cluster process in context of the finite set statistics is used to model the dynamics of the underlying process of the complex systems. In addition, we demonstrate how to reconstruct a sequence of Bayesian networks that reflect the evolution of probability dependencies between variables of the system.
Short telomeres, telomerase reverse transcriptase gene amplification, and increased telomerase activity in the blood of familial papillary thyroid cancer patients.

BACKGROUND Differentiated papillary thyroid cancer is mostly sporadic, but the recurrence of the familial form has been reported. Short or dysfunctional telomeres have been associated with familial benign diseases and familial breast cancer. OBJECTIVE The aim of our work was to study the telomere-telomerase complex in the peripheral blood of patients with familial papillary thyroid cancer (FPTC), including the measurement of relative telomere length (RTL), telomerase reverse transcriptase (hTERT) gene amplification, hTERT mRNA expression, telomerase protein activity, and search of hTERT or telomerase RNA component gene mutations. PATIENTS Cumulating a series of patients seen at the University of Siena and a series at the University of Rome, the experiments were conducted in 47 FPTC patients, 75 sporadic papillary thyroid cancer (PTC) patients, 20 patients with nodular goiter, 19 healthy subjects, and 20 unaffected siblings of FPTC patients. RESULTS RTL, measured by quantitative PCR, was significantly (P < 0.0001) shorter in the blood of FPTC patients, compared with sporadic PTCs, healthy subjects, nodular goiter subjects, and unaffected siblings. Also by fluorescence in situ hybridization analysis, the results confirmed shorter telomere lengths in FPTC patients (P = 0.01). hTERT gene amplification was significantly (P < 0.0001) higher in FPTC patients, compared with the other groups, and in particular, it was significantly (P = 0.03) greater in offspring with respect to parents. hTERT mRNA expression, as well as telomerase activity, was significantly higher (P = 0.0003 and P < 0.0001, respectively) in FPTC patients, compared with sporadic PTCs. RTL, measured in cancer tissues, was shorter (P < 0.0001) in FPTC patients, compared with sporadic PTCs. No mutations of the telomerase RNA component and hTERT genes were found. CONCLUSION Our study demonstrates that patients with FPTC display an imbalance of the telomere-telomerase complex in the peripheral blood, characterized by short telomeres, hTERT gene amplification, and expression. These features may be implicated in the inherited predisposition to develop FPTC.
Settlements, Landscapes and Identities among the Tswana of the Western Transvaal and Eastern Kalahari before 1820

This paper suggests that our appreciation of Tswana history in the 17th and 18th centuries can be improved by taking into consideration the diverse types of landscape the many Tswana groups attached themselves to. Making the argument has required generating forms of corroborating evidence: plotting settlements derived from oral traditions; linking resettlement patterns to territory with overlays of terrain, soil and water resources; measuring likely territories controlled by individual groups; using archaeological studies and the observations of early 19th-century travellers to determine the relationship of settlements to water, agricultural and grazing resources, and finally, using totemic identities as a measure of mobility as related to landscape. There appears overall to be an east-to-west pattern of landscape resources that correlates with individual Tswana settlement options. From east to west, rainfall, water and soils decline in quantity and quality, leading to greater territory deployed to sustain agriculture and grazing, with the nature of settlements adapting accordingly. The larger the territory, the greater was the incentive for leaders to use force to control or expand it. The paper seeks to refute widely held assumptions that the pre-1800 Rustenburg area in the Transvaal was suffering from increasing violence and demonstrates that Hurutshe hegemony, such as it was, could not have extended much beyond the Swartruggens area to include Rustenburg-Pilanesberg. It suggests, however, that conflict was on the rise in the pre-1800 period among the Kalahari Tswana. It also supports the broadening of archaeological analysis through the use of oral traditions, language analysis, terrain analysis and other contextual approaches, as well as the application of geographical information systems software, to historicise the archaeological record. It suggests that some Tswana groups preferred to move periodically and build smaller and more sustainable settlements rather than attach themselves to mega-sites.
CONTEXTUAL EFFECT IN SIMPLE REACTION TIME

Role of expectancy in simple reaction time was investigated by changing the context in which an imperative stimulus was presented in various foreperiods (FP's). Two experiments were conducted. In experiment I, the range from which FP's were sampled was shifted, and in experiment II, the relative frequencies of various FP's were biased. The results of both experiments supported the assumption that expectancy has an important role in simple reaction time.
Factorising the Multiple Fault Localization Problem: Adapting Single-Fault Localizer to Multi-fault Programs

Software failures are not rare and fault localizations always an important but laborious activity. Since there is no guarantee that no more than one fault exists in a faulty program, the approach to locate all the faults is necessary. Spectrum-based fault localization techniques collect dynamic program spectra as well as test results of program runs, and estimate the extent of program elements being related to fault(s). A popular solution into generate a ranked list of suspicious candidates, which are checked in order, stopping whenever a fault is found. Such single fault localizers locate one fault in one checking round, terminate, and wait to be triggered by the regression testing to validate the fixing of the located fault. In this paper, we study the manifestation of multiple faults in a program and propose an effective mechanism to indicate their presence. When a fault is reached during the checking round, we use it to interpret the failures observed, and update the indicator to judge whether there remain other faults in the program. Our indicator serves as a stopping criterion of checking the ranked list of suspicious candidates. Our work factories the multiple fault localization problem into developing single-fault localizers and adapting them to multi-fault programs. It both improves the fault localization efficiencies of single-fault localizers, and avoids the ineffective efforts of thoroughly abandoning the many single-fault localizers to develop multi-fault localizers.
In Search of ‘Birth Month Genes’: Using Existing Data Repositories to Locate Genes Underlying Birth Month-Disease Relationships

Prenatal and perinatal exposures vary seasonally (e.g., sunlight, allergens) and many diseases are linked with variance in exposure. Epidemiologists often measure these changes using birth month as a proxy for seasonal variance. Likewise, Genome-Wide Association Studies have associated or implicated these same diseases with many genes. Both disparate data types (epidemiological and genetic) can provide key insights into the underlying disease biology. We developed an algorithm that links 1) epidemiological data from birth month studies with 2) genetic data from published gene-disease association studies. Our framework uses existing data repositories — PubMed, DisGeNET and Gene Ontology — to produce a bipartite network that connects enriched seasonally varying biofactorss with birth month dependent diseases (BMDDs) through their overlapping developmental gene sets. As a proof-of-concept, we investigate 7 known BMDDs and highlight three important biological networks revealed by our algorithm and explore some interesting genetic mechanisms potentially responsible for the seasonal contribution to BMDDs.
Eya4 regulation of Na+/K+-ATPase is required for sensory system development in zebrafish

To investigate the mechanisms by which mutations in the human transcriptional co-activator EYA4 gene cause sensorineural hearing loss that can occur in association with dilated cardiomyopathy, we studied eya4 expression during zebrafish development and characterized eya4 deficiency. eya4 morphant fish embryos had reduced numbers of hair cells in the otic vesicle and lateral line neuromasts with impaired sensory responses. Analyses of candidate genes that are known to be expressed in a temporal and spatial pattern comparable to eya4 focused our analyses on atp1b2b, which encodes the β2b subunit of the zebrafish Na+/K+-ATPase. We demonstrate atp1b2b levels are reduced in eya4 morphant fish and that morpholino oligonucleotides targeting the atp1b2b gene recapitulated the eya4 deficiency phenotypes, including heart failure, decreased sensory hair cell numbers in the otic vesicle and neuromasts, and abnormal sensory responses. Furthermore, atp1b2b overexpression rescued these phenotypes in eya4 morphant fish. We conclude that eya4 regulation of Na+/K+-ATPase is crucial for the development of mechanosensory cells and the maintenance of cardiac function in zebrafish.
A Redshift Determination for XRF 020903: First Spectroscopic Observations of an X-Ray Flash

We report the discovery of optical and radio afterglow emission from the extremely soft X-ray flash XRF 020903. Our spectroscopic observations provide the first redshift for an X-ray flash, thereby setting the distance scale for these events. At z = 0.251, XRF 020903 is one of the nearest cosmic explosions ever detected, second only to the recent GRB 030329 and the unusual GRB 980425/SN 1998bw. Moreover, XRF 020903 is the first X-ray flash for which we detect an optical afterglow. The luminosity of the radio afterglow of XRF 020903 is 1000 times greater than that of Ibc supernovae but similar to those of GRB afterglows. From broadband afterglow modeling we show that the explosion energy of XRF 020903 is not dissimilar to values inferred for typical gamma-ray bursts, suggesting that these cosmological explosions may derive from a similar mechanism.
Abnormal activity in reward brain circuits in human narcolepsy with cataplexy

Hypothalamic hypocretins (or orexins) regulate energy metabolism and arousal maintenance. Recent animal research suggests that hypocretins may also influence reward‐related behaviors. In humans, the loss of hypocretin‐containing neurons results in a major sleep‐wake disorder called narcolepsy‐cataplexy, which is associated with emotional disturbances. Here, we aim to test whether narcoleptic patients show an abnormal pattern of brain activity during reward processing.
On the boundary conditions in modeling of human-like reaching movements

The paper deals with modeling of human-like reaching movements using optimal control theory. Typically, in the construction of optimization models, capturing the invariant features of human movements, the main emphasis is placed on the form of the optimality criterion. However, the boundary conditions are also an important part of the optimization problem. Considering reaching movements in the manipulation of flexible objects, we first show that the conventional imposition of the boundary conditions does not always produce a good match to the experimental data featuring the acceleration jumps in highly dynamic tasks. To explain the acceleration jumps, we reformulate the problem, using the concept of natural boundary conditions, and show that it improves the prediction of the experimental data. Finally, it is suggested how not only the acceleration but all the boundary conditions can placed in a natural way.
Lower Bounds in Real Schubert Calculus

We describe a large-scale computational experiment to study structure in the numbers of real solutions to osculating instances of Schubert problems. This investigation uncovered Schubert problems whose computed numbers of real solutions variously exhibit nontrivial upper bounds, lower bounds, gaps, and a congruence modulo four. We present a family of Schubert problems, one in each Grassmannian, and prove their osculating instances have the observed lower bounds and gaps.
Serotonin Transporter Polymorphism Modulates N-Back Task Performance and fMRI BOLD Signal Intensity in Healthy Women

Context Exploring intermediate phenotypes within the human brain's functional and structural circuitry is a promising approach to explain the relative contributions of genetics, complex behaviors and neural mechanisms in the development of major depressive disorder (MDD). The polymorphic region 5-HTTLPR in the serotonin transporter gene (SLC6A4) has been shown to modulate MDD risk, but the neural underpinnings are incompletely understood. Objective 37 right handed healthy women between 21 and 61 years of age were invited to participate in an fMRI modified n-back study. The functional polymorphism 5-HTTLPR located in the promoter region of the SLC6A4 gene was genotyped using polymerase chain reaction (PCR). Results Short 5-HTTLPR allele carriers showed more blood-oxygen-level-dependent (BOLD) bilateral prefrontal cortex activation in the right [F(2, 30) = 4.8, η2 = . 25, p = . 026] and left [F(2, 30) = 4.1, η2 = . 22, p = . 015] inferior frontal gyrus pars triangularis with increasing n-back task difficulty relative to long 5-HTTLPR allele carriers. Short 5-HTTLPR allele carriers had inferior task performance on the most difficult n-back condition [F(2, 30) = 4.9, η2 = . 26, p = . 014]. Conclusions This activation pattern found in healthy at risk individuals resembles an activation pattern that is typically found in patients suffering from acute MDD. Altered function in these areas may reflect intermediate phenotypes and may help explain the increased risk of depression in short 5-HTTLPR allele carriers.
HANDEDNESS AND LANGUAGE LATERALIZATION: WHY ARE WE RIGHT-HANDED AND LEFT-BRAINED?

Around 90% of humans prefer their right hand for unimanual actions and are left- hemisphere dominant for language functions; a pattern far from negligible. The phenomena of handedness and cerebral lateralization for language are presented along with the different theories that attempt to explain the presence of these functional asymmetries. The focus is on the adaptive advantages both on the individual and the population level. Most importantly, the intriguing question of why humans are right-handed and left-brained and not the other way around is tackled; a number of evolutionary, cultural, and genetic accounts are presented, along with theories that explain the observed pattern of asymmetries by means of the different properties of the two cerebral hemispheres.
The brain structural disposition to social interaction

Social reward dependence (RD) in humans is a stable pattern of attitudes and behaviour hypothesized to represent a favourable disposition towards social relationships and attachment as a personality dimension. It has been theorized that this long‐term disposition to openness is linked to the capacity to process primary reward. Using brain structure measures from magnetic resonance imaging, and a measure of RD from Cloninger’s temperament and character inventory, a self‐reported questionnaire, in 41 male subjects sampled from a general population birth cohort, we investigated the neuro‐anatomical basis of social RD. We found that higher social RD in men was significantly associated with increased gray matter density in the orbitofrontal cortex, basal ganglia and temporal lobes, regions that have been previously shown to be involved in processing of primary rewards. These findings provide evidence for a brain structural disposition to social interaction, and that sensitivity to social reward shares a common neural basis with systems for processing primary reward information.
COMPARISON OF BIOACTIVITIES AND COMPOSITION OF CURCUMIN-FREE TURMERIC (CURCUMA LONGA L.) OILS FROM DIFFERENT SOURCES

Composition, antioxidant capacities and cell inhibition properties of curcuminfree turmeric (Curcuma longa L.) oils from different sources were evaluated by chromatographic method, two different in vitro antioxidative activity assays (DPPH* free radical scavenging assay and reducing power assay) and two different cancer cell lines (Caco-2 and MCF-7). Turmeric oil A (TOA) contains zingiberene, turmerone, and arturmerone, while turmeric oil B (TOB) contains 1-phellandrene and α-terpinolene as the major compounds. The antioxidant tests showed that both turmeric oils possessed strong free radical scavenging activities in the DPPH* free radical scavenging assay and high reducing powers in the reducing power assay compared with standard antioxidants such as BHT and commercial rosemary oil (RO). The free radical scavenging effect of 20 μL/mL TOA is comparable to that of 70 μL/mL TOB, comparable to that of 10 mM BHT and better than that of 100 μL/mL RO (p 100 μL/mL TOB > 10 mM BHT > 100 μL/mL RO (p<0.0001). Among the complex constituents in the crude TOA, ar-turmerone, turmerone, curlone and αterpineol were isolated and found with strong antioxidant activities. The anticancer activity results showed that both turmeric oils possessed high inhibitive capacity against cancer cell lines (ie. Caco-2 and MCF-7) at 20 μL/mL.
Learning in deep architectures with folding transformations

We propose a folding transformation paradigm for supervised layer-wise learning in deep neural networks by introducing concepts of internal decision making, mapping and shatter complexity. These concepts aid in the analysis of an individual hidden transformation in a deep architecture and help to map the capabilities of the proposed folding transformations. We justify the increase of VC-dimension due to depth by showing that the extra model complexity is needed to resolve large variability in the input data for complex problems. We provide an implementation and test the architecture's performance on a classification task.