Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulators of Global Genome Repair Do Not Respond to DNA Damaging Therapy but Correlate with Survival in Melanoma

Nucleotide excision repair (NER) orchestrates the repair of helix distorting DNA damage, induced by both ultraviolet radiation (UVR) and cisplatin. There is evidence that the global genome repair (GGR) arm of NER is dysfunctional in melanoma and it is known to have limited induction in melanoma cell lines after cisplatin treatment. The aims of this study were to examine mRNA transcript levels of regulators of GGR and to investigate the downstream effect on global transcript expression in melanoma cell lines after cisplatin treatment and in melanoma tumours. The GGR regulators, BRCA1 and PCNA, were induced in melanocytes after cisplatin, but not in melanoma cell lines. Transcripts associated with BRCA1, BRCA2, ATM and CHEK2 showed altered expression in melanoma cell lines after cisplatin treatment. In melanoma tumour tissue BRCA1 transcript expression correlated with poor survival and XPB expression correlated with solar elastosis levels. Taken together, these findings provide evidence of the mechanisms underlying NER deficiency in melanoma.
Optimizing Nested Queries with Parameter Sort Orders

Nested iteration is an important technique for query evaluation. It is the default way of executing nested subqueries in SQL. Although decorrelation often results in cheaper non-nested plans, decorrelation is not always applicable for nested subqueries. Nested iteration, if implemented properly, can also win over decorrelation for several classes of queries. Decorrelation is also hard to apply to nested iteration in user-defined SQL procedures and functions. Recent research has proposed evaluation techniques to speed up execution of nested iteration, but does not address the optimization issue. In this paper, we address the issue of exploiting the ordering of nested iteration/procedure calls to speed up nested iteration. We propose state retention of operators as an important technique to exploit the sort order of parameters/correlation variables. We then show how to efficiently extend an optimizer to take parameter sort orders into consideration. We implemented our evaluation techniques on PostgreSQL, and present performance results that demonstrate significant benefits.
Decomposing attention-deficit/hyperactivity disorder (ADHD)-related effects in response speed and variability.

OBJECTIVE Slow and variable reaction times (RTs) on fast tasks are such a prominent feature of attention-deficit/hyperactivity disorder (ADHD) that any theory must account for them. However, this has proven difficult because the cognitive mechanisms responsible for this effect remain unexplained. Although speed and variability are typically correlated, it is unclear whether single or multiple mechanisms are responsible for group differences in each. RTs are a result of several semi-independent processes, including stimulus encoding, rate of information processing, speed-accuracy trade-offs, and motor response, which have not been previously well characterized. METHOD A diffusion model was applied to RTs from a forced-choice RT paradigm in two large, independent case-control samples (NCohort 1 = 214 and NCohort 2 = 172). The decomposition measured three validated parameters that account for the full RT distribution and assessed reproducibility of ADHD effects. RESULTS In both samples, group differences in traditional RT variables were explained by slow information processing speed, and unrelated to speed-accuracy trade-offs or nondecisional processes (e.g., encoding, motor response). CONCLUSIONS RT speed and variability in ADHD may be explained by a single information processing parameter, potentially simplifying explanations that assume different mechanisms are required to account for group differences in the mean and variability of RTs.
Assessing an Improved Protocol for Plasma microRNA Extraction

The first step in biomarkers discovery is to identify the best protocols for their purification and analysis. This issue is critical when considering peripheral blood samples (plasma and serum) that are clinically interesting but meet several methodological problems, mainly complexity and low biomarker concentration. Analysis of small molecules, such as circulating microRNAs, should overcome these disadvantages. The present study describes an optimal RNA extraction method of microRNAs from human plasma samples. Different reagents and commercially available kits have been analyzed, identifying also the best pre-analytical conditions for plasma isolation. Between all of them, the column-based approaches were shown to be the most effective. In this context, miRNeasy Serum/Plasma Kit (from Qiagen) rendered more concentrated RNA, that was better suited for microarrays studies and did not require extra purification steps for sample concentration and purification than phenol based extraction methods. We also present evidences that the addition of low doses of an RNA carrier before starting the extraction process improves microRNA purification while an already published carrier dose can result in significant bias over microRNA profiles. Quality controls for best protocol selection were developed by spectrophotometry measurement of contaminants and microfluidics electrophoresis (Agilent 2100 Bioanalyzer) for RNA integrity. Selected donor and patient plasma samples and matched biopsies were tested by Affymetrix microarray technology to compare differentially expressed microRNAs. In summary, this study defines an optimized protocol for microRNA purification from human blood samples, increasing the performance of assays and shedding light over the best way to discover and use these biomarkers in clinical practice.
Cooperative Distributed Multiuser MMSE Relaying in Wireless Ad-Hoc Networks

We consider a wireless ad-hoc network with single antenna nodes under a two-hop traffic pattern. Two system architectures are investigated in this paper: Either linear amplify-and-forward relays (LinRel) or a distributed antenna system with linear processing (LDAS) serve as repeaters. The gain factors of the repeaters are assigned such that the mean squared error (MSE) of the signal at the destinations is minimised (multiuser MMSE relaying). A scalar multiplier γm ∈ C at each destination m allows for received signals that are scaled and rotated versions of the transmitted symbols. We distinguish two cases: 1) The factors are equal for all destinations: γm = γ. 2) An individual factor γm is chosen for each destination m. Multiuser MMSE relaying essentially realizes a distributed spatial multiplexing gain with single antenna nodes as all source/destination pairs can communicate concurrently over the same physical channel. The main contribution of this paper is the derivation of the MMSE gain factors. We evaluate the relaying scheme in comparison to multiuser zero forcing (ZF) (1) and show that it can outperform the latter in terms of average sum rate and diversity gain. Keywords - cooperative relaying, ad-hoc networks, distributed spatial multiplexing, minimum mean squared error (MMSE)
Stereo camera based navigation of mobile robots on rough terrain

A navigation algorithm for mobile robots in unknown rough terrain has been developed. The algorithm is solely based on stereo images and suitable for wheeled and legged robots. The navigation system is able to guide the robot along a short and safe path to a goal specified by the operator and given in coordinates relative to the starting point of the robot. The algorithm uses visual odometry for localization. The terrain is modeled from stereo images and its traversability is estimated. A D* Lite planner is used for efficiently planning a short and safe path by incorporating terrain traversability in the planning process. The robot actively explores its environment as it follows the path to the goal. The algorithm has been tested on a wheel driven mobile robot and on a six-legged walking robot on rough terrain.
Contact electrification between identical materials.

Pieces of identical, atomically flat insulators separate a charge Q when brought into contact and then parted. Repeated contacts cause the magnitudes of the separated charges to increase monotonically. A theoretical model is presented that explains these phenomena by the inherent, molecular-scale fluctuations in the composition of the seemingly identical contacting surfaces.
A Neural Mechanism for the Opportunity Cost of Time

Recent interest has focused on a class of decision problems in which subjects encounter options serially and must decide when to leave an option in search of a better one, rather than directly comparing simultaneously presented options. Although such problems have a rich history in animal foraging and economics, relatively little is known about their neural substrates. Suggestively, however, a separate literature has argued that the key decision variable in these tasks – the opportunity cost of time, given by the average reward rate – may also govern behavioral vigor and may be reported by tonic dopamine (DA). In this study, we test whether this putative dopaminergic opportunity cost signal plays an analogous role in serial decisions by examining the behavior of patients with Parkinson’s disease (PD), on and off their DA replacement medication, in a patch-foraging task. In these tasks, subjects’ decisions about when to leave a depleting resource implicitly reflect their beliefs about the opportunity cost of time spent harvesting that resource. Consistent with the opportunity cost hypothesis, umedicated patients harvested longer than matched controls, and medication remediated this deficit. These effects were not explained by motor perseveration. Our results suggest a functional role for DA, and an associated cognitive deficit in PD, in a type of decision process that may be distinct from (but related to) the neuromodulator’s well studied roles in behavioral invigoration and learning from rewards. Significance Statement This study addresses two important questions whose answers are, unexpectedly, linked. First, what is the scope of cognitive functions of the neuromodulator dopamine, whose contributions – for instance, as assessed by both the motoric and more subtle cognitive deficits of patients with PD, which depletes dopamine – range from movement to reward and decision-making? Second, what are the neural mechanisms supporting an important but understudied class of problems, in which, rather than choose among a set of alternatives (like apples and oranges), one makes serial decisions about whether to stick with an option (like a job, or a mate) or seek another? We demonstrate a novel cognitive deficit in PD that integrates this function into the web of DA’s contributions.
Automatically Categorizing Written Texts by Author Gender

The problem of automatically determining the gender of a document's author would appear to be a more subtle problem than those of categorization by topic or authorship attribution. Nevertheless, it is shown that automated text categorization techniques can exploit combinations of simple lexical and syntactic features to infer the gender of the author of an unseen formal written document with approximately 80 per cent accuracy. The same techniques can be used to determine if a document is fiction or non-fiction with approximately 98 per cent accuracy.
Structure of the Epiphyte Community in a Tropical Montane Forest in SW China

Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site environmental factors were investigated. Epiphyte diversity was strongly correlated with host size (DBH, diameter at breast height), while within hosts the highest epiphyte diversity was in the middle canopy and epiphyte diversity was significantly higher in sites with canopy soil or a moss mat than on bare bark. DBH, elevation and stem height explained 22% of the total variation in the epiphyte species assemblage among hosts, and DBH was the most important factor which alone explained 6% of the variation. Within hosts, 51% of the variation in epiphyte assemblage composition was explained by canopy position and substrate, and the most important single factor was substrate which accounted for 16% of the variation. Analysis of network properties indicated that the epiphyte host community was highly nested, with a low level of epiphyte specialization, and an almost even interaction strength between epiphytes and host trees. Together, these results indicate that large trees harbor a substantial proportion of the epiphyte community in this forest.
Direct Pulp-Capping with Calcium Enriched Mixture in Primary Molar Teeth: A Randomized Clinical Trial

INTRODUCTION The aim of this trial was to compare clinical and radiographic success rates of direct pulp capping (DPC) using a novel biomaterial called Calcium Enriched Mixture (CEM) cement versus Mineral Trioxide Aggregate (MTA) in primary molar teeth. MATERIALS AND METHODS In this randomized clinical trial 42 deciduous molars in 21 patients who had at least two teeth requiring DPC, were treated. The enrolled patients were between 5-8 years. The molar teeth were randomly divided into two experimental groups. Patients and operators were blinded. The teeth were anaesthetized, caries were removed and after pinpoint exposure of dental pulp, haemostasis was achieved. The exposure points were capped with MTA or CEM cement. All teeth were restored with amalgam. Patients were recalled for the 6-month follow up. Statistical analysis was carried out using McNemar test. RESULTS Thirty-eight teeth were available for follow up (19 in each group). The radiographic evaluations did not show failure in experimental groups; however, in clinical examinations one sinus tract was found in CEM cement group. Clinical success rates in CEM cement and MTA groups were 94.8% and 100%, respectively. Dentinal bridge formation was not observed in the two experimental groups. CONCLUSION There is no significant difference between treatment outcomes of direct pulp capping with either CEM cement or MTA; therefore, both biomaterials can be used successfully for DPC in primary molar teeth.
The hierarchical sparse selection model of visual crowding

Because the environment is cluttered, objects rarely appear in isolation. The visual system must therefore attentionally select behaviorally relevant objects from among many irrelevant ones. A limit on our ability to select individual objects is revealed by the phenomenon of visual crowding: an object seen in the periphery, easily recognized in isolation, can become impossible to identify when surrounded by other, similar objects. The neural basis of crowding is hotly debated: while prevailing theories hold that crowded information is irrecoverable – destroyed due to over-integration in early stage visual processing – recent evidence demonstrates otherwise. Crowding can occur between high-level, configural object representations, and crowded objects can contribute with high precision to judgments about the “gist” of a group of objects, even when they are individually unrecognizable. While existing models can account for the basic diagnostic criteria of crowding (e.g., specific critical spacing, spatial anisotropies, and temporal tuning), no present model explains how crowding can operate simultaneously at multiple levels in the visual processing hierarchy, including at the level of whole objects. Here, we present a new model of visual crowding—the hierarchical sparse selection (HSS) model, which accounts for object-level crowding, as well as a number of puzzling findings in the recent literature. Counter to existing theories, we posit that crowding occurs not due to degraded visual representations in the brain, but due to impoverished sampling of visual representations for the sake of perception. The HSS model unifies findings from a disparate array of visual crowding studies and makes testable predictions about how information in crowded scenes can be accessed.
Integral Field Spectroscopy of the Extended Emission-Line Region of 4C 37.43

We present Gemini integral field spectroscopy and Keck II long-slit spectroscopy of the extended emission-line region (EELR) around the quasar 4C 37.43. The velocity structure of the ionized gas is complex and cannot be explained globally by a simple dynamical model. The spectra from the clouds are inconsistent with shock or "shock + precursor" ionization models, but they are consistent with photoionization by the quasar nucleus. The best-fit photoionization model requires a low-metallicity [12 + log(O/H) ≲ 8.7] two-phase medium, consisting of a matter-bounded diffuse component with a unity filling factor (N ~ 1 cm-3, T ~ 15,000 K), in which are embedded small, dense clouds (N ~ 400 cm-3, T ~ 104 K). The high-density clouds are transient and can be regenerated through compressing the diffuse medium by low-speed shocks (VS ≲ 100 km s-1). Our photoionization model gives a total mass for the ionized gas of about 3 × 1010 M☉, and the total kinetic energy implied by this mass and the observed velocity field is ~2 × 1058 erg. The fact that luminous EELRs are confined to steep-spectrum radio-loud QSOs, yet show no morphological correspondence to the radio jets, suggests that the driving force producing the 4C 37.43 EELR was a roughly spherical blast wave initiated by the production of the jet. That such a mechanism seems capable of ejecting a mass comparable to that of the total interstellar medium of the Milky Way suggests that "quasar-mode" feedback may indeed be an efficient means of regulating star formation in the early universe.
Prior-Cancer Diagnosis in Men with Nonmetastatic Prostate Cancer and the Risk of Prostate-Cancer-Specific and All-Cause Mortality

Purpose. We evaluated the impact a prior cancer diagnosis had on the risk of prostate-cancer-specific mortality (PCSM) and all-cause mortality (ACM) in men with PC. Methods. Using the SEER data registry, 166,104 men (median age: 66) diagnosed with PC between 2004 and 2007 comprised the study cohort. Competing risks and Cox regression were used to evaluate whether a prior cancer diagnosis impacted the risk of PCSM and ACM adjusting for known prognostic factors PSA level, age at and year of diagnosis, race, and whether PC treatment was curative, noncurative, or active surveillance (AS)/watchful waiting (WW). Results. At a median followup of 2.75 years, 12,453 men died: 3,809 (30.6%) from PC. Men with a prior cancer were followed longer, had GS 8 to 10 PC more often, and underwent WW/AS more frequently (P < 0.001). Despite these differences that should increase the risk of PCSM, the adjusted risk of PCSM was significantly decreased (AHR: 0.66 (95% CI: (0.45, 0.97); P = 0.033), while the risk of ACM was increased (AHR: 2.92 (95% CI: 2.64, 3.23); P < 0.001) in men with a prior cancer suggesting that competing risks accounted for the reduction in the risk of PCSM. Conclusion. An assessment of the impact that a prior cancer has on life expectancy is needed at the time of PC diagnosis to determine whether curative treatment for unfavorable-risk PC versus AS is appropriate.
Potentiation of Natural Killer Cells for Cancer Immunotherapy: A Review of Literature

It is widely acknowledged that the human immune system plays a crucial role in preventing the formation and progression of innumerable types of cancer (1). The mechanisms by which this occurs are numerous, including contributions from both the innate and adaptive immune systems. As such, immunotherapy has long been believed to be an auspicious solution in the treatment of malignancy (2). Recent research has highlighted the promise of natural killer (NK) cells as a more directed immunotherapy approach. This paper will focus on the methods of potentiation of NK cells for their use in cancer therapy.
Superstar Extinction

We estimate the magnitude of spillovers generated by 112 academic "superstars" who died pre- maturely and unexpectedly, thus providing an exogenous source of variation in the structure of their collaborators&apos; coauthorship networks. Following the death of a superstar, we find that collaborators experience, on average, a lasting 5 to 8% decline in their quality-adjusted publication rates. By exploring interactions of the treatment effect with a variety of star, coauthor and star/coauthor dyad characteristics, we seek to adjudicate between plausible mechanisms that might explain this finding. Taken together, our results suggest that spillovers are circumscribed in idea space, but less so in physical or social space. In particular, superstar extinction reveals the boundaries of the scientific field to which the star contributes -- the "invisible college. "
Simultaneous detection of prominent points on breast cancer conservative treatment images

Breast Cancer Conservative Treatment (BCCT) is now the preferred technique for breast cancer treatment. The limited reproducibility of standard aesthetic evaluation methods led to the development of objective methods, such as Breast Cancer Conservative Treatment.cosmetic results (BCCT.core) software tool. Although the satisfying results, there are still limitations concerning complete automation and the inability to measure volumetric information. With the fundamental premise of maintaining the system as a low-cost tool, the incorporation of the Microsoft Kinect sensor in BCCT evaluations was studied. The aim with this work is to enable the simultaneous detection of breast contour and breast peak points using depth-map data. Experimental results show that the proposed algorithm is accurate and robust for a wide number of patients. Additionally, comparatively to previous research, the procedure for detecting prominent points was automated.
Long‐Term Estimation of Diurnal Vertical E × B Drift Velocities Using C/NOFS and Ground‐Based Magnetometer Observations

We report on the development of a new mathematical expression to estimate local daytime (0700–1700 LT) vertical E × B drift in low latitudes using a combination of ground‐based magnetometer measurements and Communications and Navigation Outage Forecasting System (C/NOFS) satellite observations. The expression was developed over Jicamarca (11.8°S, 77.2°W; 0.8°N geomagnetic) and validated with Jicamarca Unattended Long‐Term studies of the Ionosphere and Atmosphere (JULIA) mode and incoherent scatter radar (ISR) measurements during the period 2008–2014. The obtained correlation coefficient (R) values computed using observed and derived vertical E × B drift velocities are 0.79 and 0.84 for ISR and JULIA, respectively when data are available during 2008–2014. Storm‐time comparison between observed and derived vertical E × B drift velocities agreed well with R of 0.92 and 0.87 during 5–8 August 2011 and 8–11 March 2012 geomagnetic storm periods for ISR and JULIA observations, respectively. Overall, we found that the developed expression is applicable in estimating vertical E × B drift response during quiet and geomagnetic storm periods. Based on these findings, we suggest that it is possible to develop accurate daytime global vertical E × B drift model over the equatorial latitude regions using inexpensive magnetometer observations and available satellite data.