Miracle-dz/UniFAR-FTUs huggingface dataset:
The Chlamydomonas reinhardtii Molybdenum Cofactor Enzyme crARC Has a Zn-Dependent Activity and Protein Partners Similar to Those of Its Human Homologue

ABSTRACT The ARC (amidoxime reducing component) proteins are molybdenum cofactor (Moco) enzymes named hmARC1 and hmARC2 (human ARCs [hmARCs]) in humans and YcbX in Escherichia coli. They catalyze the reduction of a broad range of N-hydroxylated compounds (NHC) using reducing power supplied by other proteins. Some NHC are prodrugs or toxic compounds. YcbX contains a ferredoxin (Fd) domain and requires the NADPH flavin reductase CysJ to reduce NHC. In contrast, hmARCs lack the Fd domain and require a human cytochrome b5 (hCyt b5) and a human NADH Cyt b5 reductase (hCyt b5-R) to reduce NHC. The ARC proteins in the plant kingdom are uncharacterized. We demonstrate that Chlamydomonas reinhardtii mutants defective in Moco biosynthesis genes are sensitive to the NHC N6-hydroxylaminopurine (HAP). The Chlamydomonas reinhardtii ARC protein crARC has been purified and characterized. The six Chlamydomonas Fds were isolated, but none of them are required by crARC to reduce HAP. We have also purified and characterized five C. reinhardtii Cyt b5 (crCyt b5) and two flavin reductases, one that is NADPH dependent (crCysJ) and one that is NADH dependent (crCyt b5-R). The data show that crARC uses crCyt b5-1 and crCyt b5-R to reduce HAP. The crARC has a Zn-dependent activity, and the presence of Zn increases its Vmax more than 14-fold. In addition, all five cysteines of crARC were substituted by alanine, and we demonstrate that the fully conserved cysteine 252 is essential for both Moco binding and catalysis. Therefore, it is proposed that crARC belongs to the sulfite oxidase family of Moco enzymes.
It's Time to Revise the Definition of Status Epilepticus

Generalized, tonic-clonic status epilepticus is well recognized as a common neurologic emergency requir- ing prompt treatment. The diagnosis is usually not diffi- cult, other than for patients with prolonged seizures, who often develop increasingly subtle clinical features (1,2). There also appears to be a consensus among physicians regarding treatment (3). Nonetheless, there is a major, persistent dilemma regarding status epilepticus: its defi- nition. Discussions concerning the precise definition of status epilepticus all too often result in agreement that current “textbook” definitions are either imprecise, at odds with clinical practice, or both. Here we propose a revised system for defining status epilepticus that ad- dresses these problems. References to status epilepticus prior to the mid- 19th century focused on cases in which seizures lasted many hours to days (4). In 1904, Clark and Prout (5) defined status epilepticus as a state in which seizures occur so frequently that ‘‘the coma and exhaustion are continuous between the seizures. ” In his general textbook of neu- rology published in 1940, Kinnier Wilson (6) referred to status epilepticus as the severest form of seizures in which “the post-convulsive sleep of one attack is cut short by development of the next. ” Aspects of these definitions were mirrored in the first International Clas- sification of Epileptic Seizures that was developed in 1964 by the International League Against Epilepsy (ILAE). Status epilepticus was defined as the situation in which “a seizure persists for a sufficient length of time or is repeated frequently enough to produce a fixed and enduring epileptic condition” (7). The same definition was retained in the revised classification published in 1970 (8), and it was modified slightly in 1981 to refer to the situation in which “a seizure persists for a sufficient length of time or is repeated frequently enough that re- covery between attacks does not occur” (9).
Detecting unique column combinations on dynamic data

The discovery of all unique (and non-unique) column combinations in an unknown dataset is at the core of any data profiling effort. Unique column combinations resemble candidate keys of a relational dataset. Several research approaches have focused on their efficient discovery in a given, static dataset. However, none of these approaches are suitable for applications on dynamic datasets, such as transactional databases, social networks, and scientific applications. In these cases, data profiling techniques should be able to efficiently discover new uniques and non-uniques (and validate old ones) after tuple inserts or deletes, without re-profiling the entire dataset. We present the first approach to efficiently discover unique and non-unique constraints on dynamic datasets that is independent of the initial dataset size. In particular, Swan makes use of intelligently chosen indices to minimize access to old data. We perform an exhaustive analysis of Swan and compare it with two state-of-the-art techniques for unique discovery: Gordian and Ducc. The results show that Swan significantly outperforms both, as well as their incremental adaptations. For inserts, Swan is more than 63x faster than Gordian and up to 50x faster than Ducc. For deletes, Swan is more than 15x faster than Gordian and up to 1 order of magnitude faster than Ducc. In fact, Swan even improves on the static case by dividing the dataset into a static part and a set of inserts.
Supplemented dialysis: amino acid-based solutions in peritoneal dialysis.

Peritoneal dialysis is associated with several metabolic and nutritional abnormalities, some of which are related to the use of glucose-based solutions. Furthermore, the catabolic effects of uremia per se, protein and amino acid losses into the dialysate, peritonitis and poor appetite contribute to amino acid abnormalities, negative nitrogen balance and a high prevalence of malnutrition in peritoneal dialysis patients. To overcome these problems the use of amino acid instead of glucose as an osmotic agent has been proposed. Short-term studies have shown that amino acid-based solutions in peritoneal dialysis may supplement in excess the daily losses of amino acids during dialysis with glucose-based solutions. The amino acid solutions produce similar ultrafiltration and solute transport as the standard glucose solutions although the period of effective ultrafiltration is rather short. However, it should be noted that some studies have reported that the transport of small and large solutes may increase in patients using amino acid solutions. During the early 1980s several investigators have developed and tested different amino acid solutions for peritoneal dialysis. The initial clinical experience from Toronto with amino acid solutions containing large amounts of non-essential amino acids and inadequate amount of buffer were in general discouraging. The patients, who were not always malnourished and tended to have a low energy intake, developed increased BUN levels, acidosis, no improvement in nutritional status or amino acid abnormalities and, in some cases, anorexia. In 1985 a new 1% amino acid solution, containing an increased buffer amount and amino acids (mainly essential) in proportions which take the amino acid abnormalities in uremic patients into account, became available. The use of this solution resulted in some improvement in amino acid pattern and nutritional parameters, but acidosis and increased BUN levels remained problems. The experiences from these and previous studies showed that: (1) the improvement of the composition of amino acid solutions was beneficial; (2) a further increase of the buffer amount was needed; (3) patients included should have signs of protein malnutrition combined with low dietary protein intake to benefit from intraperitoneal amino acid supply, and (4) energy intake should be sufficient to prevent amino acids to end up as energy source. For this purpose a new improved 1.1% amino acid solution has been developed containing a further increase of some essential amino acids and an increased amount of lactate (40 mmol/l). This solution has been tested in malnourished patients eating 0.8 g protein/kg/day and 25-30 kcal/kg/day. (ABSTRACT TRUNCATED AT 400 WORDS)
CaMKII in sinoatrial node physiology and dysfunction

The calcium and calmodulin-dependent protein kinase II (CaMKII) is present in sinoatrial node (SAN) pacemaker cells and is required for physiological “fight or flight” SAN beating rate responses. Inhibition of CaMKII in SAN does not affect baseline heart rate, but reduces heart rate increases in response to physiological stress. CaMKII senses intracellular calcium (Ca2+) changes, oxidation status, and hyperglycemia to phosphorylate substrates that regulate Ca2+-sensitive proteins, such as L-type Ca2+ channels, phospholamban, and cardiac ryanodine receptors (RyR2). All of these substrates are involved in the SAN pacemaking mechanism. Excessive CaMKII activity, as occurs under pathological conditions such as heart failure, ischemia, and diabetes, can promote intracellular Ca2+ overload and reactive oxygen species production. Oxidation of CaMKII (ox-CaMKII) locks CaMKII into a constitutively active configuration that contributes to SAN cell apoptosis and fibrosis. This ox-CaMKII-mediated loss of functional SAN cells contributes to SAN dysfunction (SND) and sudden death. Thus, CaMKII has emerged as a central regulator of physiological SAN responses and a key determinant of SND.
Improving the Efficiency of GPGPU Work-Queue Through Data Awareness

The architecture and programming model of current GPGPUs are best suited for applications that are dominated by structured control and data flows across large regular datasets. Parallel workloads with irregular control and data structures cannot easily harness the processing power of the GPGPU. One approach for mapping these irregular-parallel workloads to GPGPUs is using work-queues. The work-queue approach improves the utilization of SIMD units by only processing useful works that are dynamically generated during execution. As current GPGPUs lack necessary supports for work-queues, a software-based work-queue implementation often suffers from memory contention and load balancing issues. In this article, we present a novel hardware work-queue design named DaQueue, which incorporates three data-aware features to improve the efficiency of work-queues on GPGPUs. We evaluate our proposal on the irregular-parallel workloads and carry out a case study on a path tracing pipeline with a cycle-level simulator. Experimental results show that for the tested workloads, DaQueue improves performance by 1.53× on average and up to 1.91×. Compared to a hardware worklist approach that is the state-of-the-art prior work, DaQueue can achieve an average of 33.92% extra speedup with less hardware area cost.
Mechanical, optical and barrier properties of PLA-layered silicate nanocomposites coated with organic plasma polymer thin films

In the frame of the efforts that are nowadays provided to develop new environmentally-friendly products as biosourced alternative to petrochemical polymers, we investigated in this work new PLA-based materials for packaging applications obtained by combining bulk and surface modifications of PLA substrates. Four PLA-based nanocomposites were prepared by adding organo-modified layered silicates (either Cloisite® 30B or Cloisite® 20A) and a nucleating agent, i.e. N,N’-ethylenebisstearamide (EBS). The combination of EBS with CL30B led to very good nanofiller dispersion into PLA-clay nanocomposite while allowing, unlike neat PLA, to preserve the structural and thermal properties of PLA under plasma treatment. Based on this study, PLA/CL30B/EBS nanocomposites have been selected to investigate their surface modification that consisted in depositing on this substrate an organic barrier coating, i.e. an ethyl lactate plasma polymer film (ELPPF) synthesized by plasma polymerization of ethyl lactate. The PLA/CL30B/EBSELPPF system allowed increasing the tensile modulus from 3800 MPa (uncoated film) to 5200 MPa at high power plasma while preserving the ultimate mechanical properties. In addition, optical properties study showed that PLA/CL30B/EBS-ELPPF is also the best UV-B protective material while keeping a good transparency. Finally, the oxygen transmission rate was reduced by 53% with respect to neat PLA. All properties of final material are discussed as a function of the characteristics of PLA-clay nanocomposite substrate, of the ethyl lactate plasma polymer film (ELPPF) and of the substrate/plasma film interface.
Statistical Frailty Modeling for Quantitative Analysis of Exocytotic Events Recorded by Live Cell Imaging: Rapid Release of Insulin-Containing Granules Is Impaired in Human Diabetic β-cells

Hormones and neurotransmitters are released when secretory granules or synaptic vesicles fuse with the cell membrane, a process denoted exocytosis. Modern imaging techniques, in particular total internal reflection fluorescence (TIRF) microscopy, allow the investigator to monitor secretory granules at the plasma membrane before and when they undergo exocytosis. However, rigorous statistical approaches for temporal analysis of such exocytosis data are still lacking. We propose here that statistical methods from time-to-event (also known as survival) analysis are well suited for the problem. These methods are typically used in clinical settings when individuals are followed over time to the occurrence of an event such as death, remission or conception. We model the rate of exocytosis in response to pulses of stimuli in insulin-secreting pancreatic β-cell from healthy and diabetic human donors using piecewise-constant hazard modeling. To study heterogeneity in the granule population we exploit frailty modeling, which describe unobserved differences in the propensity to exocytosis. In particular, we insert a discrete frailty in our statistical model to account for the higher rate of exocytosis in an immediately releasable pool (IRP) of insulin-containing granules. Estimates of parameters are obtained from maximum-likelihood methods. Since granules within the same cell are correlated, i.e., the data are clustered, a modified likelihood function is used for log-likelihood ratio tests in order to perform valid inference. Our approach allows us for example to estimate the size of the IRP in the cells, and we find that the IRP is deficient in diabetic cells. This novel application of time-to-event analysis and frailty modeling should be useful also for the study of other well-defined temporal events at the cellular level.
Positive Allosteric Modulator of GABA Lowers BOLD Responses in the Cingulate Cortex

Knowledge about the neural underpinnings of the negative blood oxygen level dependent (BOLD) responses in functional magnetic resonance imaging (fMRI) is still limited. We hypothesized that pharmacological GABAergic modulation attenuates BOLD responses, and that blood concentrations of a positive allosteric modulator of GABA correlate inversely with BOLD responses in the cingulate cortex. We investigated whether or not pure task-related negative BOLD responses were co-localized with pharmacologically modulated BOLD responses. Twenty healthy adults received either 5 mg diazepam or placebo in a double blind, randomized design. During fMRI the subjects performed a working memory task. Results showed that BOLD responses in the cingulate cortex were inversely correlated with diazepam blood concentrations; that is, the higher the blood diazepam concentration, the lower the BOLD response. This inverse correlation was most pronounced in the pregenual anterior cingulate cortex and the anterior mid-cingulate cortex. For subjects with diazepam plasma concentration > 0.1 mg/L we observed negative BOLD responses with respect to fixation baseline. There was minor overlap between cingulate regions with task-related negative BOLD responses and regions where the BOLD responses were inversely correlated with diazepam concentration. We interpret that the inverse correlation between the BOLD response and diazepam was caused by GABA-related neural inhibition. Thus, this study supports the hypothesis that GABA attenuates BOLD responses in fMRI. The minimal overlap between task-related negative BOLD responses and responses attenuated by diazepam suggests that these responses might be caused by different mechanisms.
Mechanism of activation of an N‐ras gene in the human fibrosarcoma cell line HT1080.

A full length N‐ras gene has been cloned from both the human fibrosarcoma cell line HT1080 and from normal human DNA. N‐ras isolated from HT1080 will efficiently induce morphological transformation of NIH/3T3 cells in a transfection assay, whereas N‐ras isolated from normal human DNA has no effect on NIH/3T3 cells. The coding regions of the normal N‐ras gene have been sequenced and the predicted amino acid sequence of the N‐ras product is very similar to that of the c‐Ha‐ras1 and c‐Ki‐ras2 products. By making chimeric molecules between the two cloned genes the activating alteration in the HT1080 N‐ras gene has been localised to a single base change that results in an amino acid alteration at position 61 of the p21 N‐ras product.
House of Green Cards

This study contributes to the labor market inequality and organizations literature by investigating the role that government agents play in shaping the employment of immigrants. Using unique data on applications for immigrant permanent labor certification evaluated by U.S. Department of Labor agents, we assess to what extent immigrants of select citizenship groups experience disparities in the labor certification process—one critical stage of the work authorization system leading to the granting of most employment-based green cards. Despite current U.S. laws that forbid discrimination on the basis of nationality, we find that labor certification approvals differ significantly depending on immigrants’ foreign citizenship, even after controlling for key factors. Additionally, because of the U.S. government’s unique process of auditing applications, we are in a rare position to empirically distinguish between statistical and preference-based accounts of labor market discrimination in the labor certification process. In support of the statistical account, we find that certification approvals are equally likely for immigrant workers from the vast majority of citizenship groups when agents review audited applications with detailed employment information. This article concludes by discussing the implications of our results for addressing disparities in the employment of foreign nationals.
Closer Look at the Baseflow Correlation Method

In 2003, Reilly and Kroll examined the baseflow correlation method at river sites throughout the United States. The current study reexamines Reilly and Kroll’s baseflow correlation experiment by investigating the use of different performance metrics, experimental parameters, and model assumptions that were not investigated by Reilly and Kroll. The goal of this study is to provide additional guidance on how to implement the baseflow correlation method in practice. The results confirm that baseflow measurements should be obtained during low flow seasons and as far as possible from runoff events. When one has only five baseflow measurements at the low-flow partial-record site, the correlation coefficient between baseflows at gauged and low-flow partial-record sites should be at least 0.9; when the number of baseflow measurements is 10 or more, the method performs adequately if the correlation coefficient is greater than 0.6. The performance of the baseflow correlation method improves as the number of baseflo.
Disgerising personal inventories: a situated identity strategy

The problems associated with disguise in scale construction are approached from the perspective of situated identity theory. Procedures are proposed to determine empirically the communicable meaning of scale-item responses, to measure precisely the dimensions along which responses are potentially reactive. The utility of the approach is assessed in a series of studies employing various response formats for Machiavellian scale items. Contrary to conclusions suggested by previous research employing groups of items, the data reveal that a simple, forced-choice format provides maximum disguise and minimal bias-but only if these forced-choice items are embedded among other items of extraneous content. The possibilities for extension of the approach are discussed.
Temporal Network Comparison using Graphlet-orbit Transitions

Networks are widely used to model real-world systems and uncover their topological features. Network properties such as the degree distribution and shortest path length have been computed in numerous real-world networks, and most of them have been shown to be both scale-free and small-world networks. Graphlets and network motifs are subgraph patterns that capture richer structural information than aforementioned global network properties, and these local features are often used for network comparison. However, past work on graphlets and network motifs is almost exclusively applicable only for static networks. Many systems are better represented as temporal networks which depict not only how a system was at a given stage but also how they evolved. Time-dependent information is crucial in temporal networks and, by disregarding that data, static methods can not achieve the best possible results. This paper introduces an extension of graphlets for temporal networks. Our proposed method enumerates all 4-node graphlet-orbits in each network-snapshot, building the corresponding orbit-transition matrix in the process. Our hypothesis is that networks representing similar systems have characteristic orbit transitions which better identify them than simple static patterns, and this is assessed on a set of real temporal networks split into categories. In order to perform temporal network comparison we put forward an orbit-transition-agreement metric (OTA). OTA correctly groups a set of temporal networks that both static network motifs and graphlets fail to do so adequately. Furthermore, our method produces interpretable results which we use to uncover characteristic orbit transitions, and that can be regarded as a network-fingerprint.