Miracle-dz/UniFAR-FTUs huggingface dataset:
Direct amifostine effect on renal tubule cells in rats.

Clinical trials indicate that amifostine offers protection against cisplatin-induced nephrotoxicity. It is unclear whether a direct pharmacological t on renal tubular cells is involved. We investigated the effect of amifostine pretreatment on the tubular apparatus and evaluated its nephroprotective potential. A total of 32 rats were treated by i.p. administration of 0.9% saline solution (group 1), 5 mg/kg cisplatin (group 2), 25 mg/kg amifostine (group 3), and 25 mg/kg amifostine followed by 5 mg/kg cisplatin (group 4) after 30 min. We recorded elevation of N-acetyl-beta-D-glucosaminidase (NAG) in 24 h pooled urine as a specific marker for tubular lesions, renal leakage of magnesium as an unspecific nephrotoxicity marker, and survival over a 10-day observation period. A significant (P < 0.002) increase in urinary NAG after treatment was documented only in cisplatin-treated group 2 [day 2 (mean+/-SE), 93+/-2.1 units/gram creatinine; day 4, 70.6+/-16 units/gram creatinine; normalization at day 8]. Treatment with amifostine before cisplatin administration resulted in a slight urinary NAG leakage (day 2, 2.8+/-1.8 units/gram creatinine; day 4, 13.8+/-13 units/gram creatinine; normalization at day 6). No increase in urinary enzyme levels was seen in the other groups, and there were no significant differences in urinary magnesium between all groups. Four of eight rats in the cisplatin-treated group and one of eight rats in the amifostine plus cisplatin-treated group died.
Fluorescence recordings of electrical activity in goldfish optic tectum in vitro

Optical methods for recording electrical activity in the goldfish optic tectum were evaluated. Tectal slices, with a short section of the optic nerve attached, were stained with a fluorescent styryl dye. Potential- dependent fluorescence changes following optic nerve stimulation were monitored with a photodiode. We found that large optical signals could be obtained. Experimental manipulations of the slice bathing solution permitted us to identify several events that contributed to the optical response, including activity in afferent fibers, excitatory and inhibitory postsynaptic potentials, and presumptive glial depolarizations. These results suggest that voltage-sensitive dyes can provide a useful alternative method for monitoring synaptic responses in the goldfish tectum, and may prove valuable in studying changes in the functional synaptic organization of the tectum following manipulations of the retinotectal pathway.
Nitric oxide may contribute to nocturnal hemodynamic changes in cirrhotic patients

OBJECTIVE:Patients with liver cirrhosis have a nocturnal worsening of hemodynamic parameters that has been associated with an increased risk of variceal bleeding at nighttime. The aim of this study was to investigate whether nitric oxide and cytokines are implicated in these hemodynamic changes.METHODS:Ten cirrhotic patients and eight controls were studied. Mean blood pressure, heart rate, plasma norepinephrine, tumor necrosis factor α and interleukin-6 levels, and serum nitrite + nitrate levels were determined at 0800, 1600, and 2400 h. All determinations were performed in supine rest and at least 4 h after meals. In a second study, nitrite + nitrate levels were assessed in 10 cirrhotic patients before and after eating a standard meal.RESULTS:Mean arterial pressure levels that were always lower in the patient group showed a nocturnal decrease in both groups of subjects. Heart rate values that were always higher in cirrhotic patients showed a nocturnal fall in controls, whereas cirrhotics maintained elevated values at nighttime. Norepinephrine levels were higher in cirrhotics and maintained similar values during the study, whereas controls had a significant nocturnal decrease. Nitrite + nitrate levels that were higher in cirrhotic patients showed a significant mean increase of 40% from morning (0800 h) to night (2400 h) in the patient group, whereas in controls no change was observed (p < 0.05). Tumor necrosis factor α and interleukin-6 levels did not change either in patients or controls during the entire period. Cirrhotic patients with or without ascites maintained a pattern of hemodynamic and biochemical changes similar to the pattern observed in the entire group of patients. Finally, no changes in serum nitrite + nitrate levels were observed in patients before and after eating the standard meal.CONCLUSION:An increased nocturnal nitric oxide production might contribute to the hemodynamic changes observed in cirrhotic patients during nighttime.
An approach to service provisioning with quality of service requirements in ATM networks

We present an approach to service provisioning with quality of service (QoS) requirements in ATM networks. The ATM network provides a set of services. Each service is characterized by its one way route, its resources (bandwidth and buffers) along the route, its input traffic constraints, and its provided QoS defined by the maximum percentage of cell loss and the maximum end-to-end cell delay. The network sets prices for its resources and users respond by requesting a resource allocation that guarantees their QoS requirements and maximizes a social welfare function consisting of the network's revenue and the users' surplus. The network adjusts the prices to maximize the welfare function and also to guarantee that the allocated resources do not exceed the available resources. Based on these prices, users request a new allocation and the network adjusts again the prices based on the new allocation. The above procedure is iterative and is shown to converge to an optimal resource allocation that maximizes the welfare function and satisfies the QoS requirements for the offered services, without exceeding the available resources. The service provisioning procedure has the following features: (i) the network needs to know only the average request rate for each type of service, their route and the resources requested by the users; (ii) users need to know only their private information (input traffic constraints and QoS requirements), their route, and the prices for resources announced by the network.
A Low-Power Single-Input Level Shifter for Oxide Thin-Film Transistors

A new level shifter circuit suitable for implementation using n-channel oxide thin-film transistors (TFTs) is reported. This level shifter is designed to convert a single 10 V input signal into a 20 V output signal. In order to raise the output voltage up to VDD in spite of the large zero- VGS current of the oxide TFT, negative VGS is applied to the pull-down TFTs. Simulation and fabrication results show that the level shifter operates correctly with oxide TFTs and that the power consumption is as low as 0.2 mW at an input signal frequency of 10 kHz.
Ventral and dorsal streams in the evolution of speech and language

The brains of humans and old-world monkeys show a great deal of anatomical similarity. The auditory cortical system, for instance, is organized into a ventral and a dorsal pathway in both species. A fundamental question with regard to the evolution of speech and language (as well as music) is whether human and monkey brains show principal differences in their organization (e.g., new pathways appearing as a result of a single mutation), or whether species differences are of a more subtle, quantitative nature. There is little doubt about a similar role of the ventral auditory pathway in both humans and monkeys in the decoding of spectrally complex sounds, which some authors have referred to as auditory object recognition. This includes the decoding of speech sounds (“speech perception”) and their ultimate linking to meaning in humans. The originally presumed role of the auditory dorsal pathway in spatial processing, by analogy to the visual dorsal pathway, has recently been conceptualized into a more general role in sensorimotor integration and control. Specifically for speech, the dorsal processing stream plays a role in speech production as well as categorization of phonemes during on-line processing of speech.
Asymptotic Degree Distribution of a Duplication–Deletion Random Graph Model

We study a discrete–time duplication–deletion random graph model and analyse its asymptotic degree distribution. The random graphs consists of disjoint cliques. In each time step either a new vertex is brought in with probability 0 < p < 1 and attached to an existing clique, chosen with probability proportional to the clique size, or all the edges of a random vertex are deleted with probability 1 − p. We prove almost sure convergence of the asymptotic degree distribution and find its exact values in terms of a hypergeometric integral, expressed in terms of the parameter p. In the regime we show that the degree sequence decays exponentially at rate , whereas it satisfies a power–law with exponent if . At the threshold the degree sequence lies between a power–law and exponential decay.
Psychosocial Stress and Cardiovascular Disease Risk: The Role of Physical Activity

Chronic stress and depression are associated with increased risk of cardiovascular disease and poorer prognosis, and physical (in)activity may be a key underlying biobehavioral mechanism. Physical activity has antidepressant effects, and physically fitter, more active individuals seem to be more biologically resilient to psychosocial stressors. This article will present data from a series of population cohort studies and laboratory-based psychophysiological studies to explore the role of physical activity as a protective factor against the effects of psychosocial stress on cardiovascular disease. These mechanisms may improve the treatment and prevention of stress-related illnesses and, thus, has important implications for public health and clinical care of high-risk patients.
Aging in personal and social immunity: do immune traits senesce at the same rate?

Summary How much should an individual invest in immunity as it grows older? Immunity is costly and its value is likely to change across an organism's lifespan. A limited number of studies have focused on how personal immune investment changes with age in insects, but we do not know how social immunity, immune responses that protect kin, changes across lifespan, or how resources are divided between these two arms of the immune response. In this study, both personal and social immune functions are considered in the burying beetle, Nicrophorus vespilloides. We show that personal immune function declines (phenoloxidase levels) or is maintained (defensin expression) across lifespan in nonbreeding beetles but is maintained (phenoloxidase levels) or even upregulated (defensin expression) in breeding individuals. In contrast, social immunity increases in breeding burying beetles up to middle age, before decreasing in old age. Social immunity is not affected by a wounding challenge across lifespan, whereas personal immunity, through PO, is upregulated following wounding to a similar extent across lifespan. Personal immune function may be prioritized in younger individuals in order to ensure survival until reproductive maturity. If not breeding, this may then drop off in later life as state declines. As burying beetles are ephemeral breeders, breeding opportunities in later life may be rare. When allowed to breed, beetles may therefore invest heavily in “staying alive” in order to complete what could potentially be their final reproductive opportunity. As parental care is important for the survival and growth of offspring in this genus, staying alive to provide care behaviors will clearly have fitness payoffs. This study shows that all immune traits do not senesce at the same rate. In fact, the patterns observed depend upon the immune traits measured and the breeding status of the individual.
The Behavior of Organic Phosphorus under Non-Point Source Wastewater in the Presence of Phototrophic Periphyton

To understand the role of ubiquitous phototrophic periphyton in aquatic ecosystem on the biogeochemical cycling of organic phosphorus, the conversion and removal kinetic characteristics of organic phosphorus (Porg) such as adenosine triphosphate (ATP) were investigated in the presence of the periphyton cultured in artificial non-point source wastewater. The preliminary results showed that the periphyton was very powerful in converting Porg evidenced by the fact that inorganic phosphorus (Pinorg) content in solution increased from about 0.7 to 14.3 mg P L−1 in 48 hours in the presence of 0.6 g L−1 periphyton. This was because the periphyton could produce abundant phosphatases that benefited the conversion of Porg to Pinrog. Moreover, this conversion process was described more suitable by the pseudo-first-order kinetic model. The periphyton was also effective in removing Porg, which showed that the Porg can be completely removed even when the initial Porg concentration was as high as 13 mg P L−1 in 48 hours in the presence of 1.6 g L−1 periphyton. Furthermore, it was found that biosorption dominated the Porg removal process and exhibited the characteristics of physical adsorption. However, this biosorption process by the periphyton was significantly influenced by biomass (absorbent dosage) and temperature. This work provides insights into Porg biogeochemical circulation of aquatic ecosystem that contained the periphyton or similar microbial aggregates.
Voting But for the Law: Evidence from Virginia on Photo Identification Requirements

One contentious question in contemporary election administration is the impact of voter identification requirements. We study a Virginia law that allows us to isolate the impact of requiring voters to show photo identification. Using novel, precinct-level data, we find that the percentage of registered voters without a driver's license and over age 85 are both positively associated with the number of provisional ballots cast due to a lack of a photo ID. To examine the law's impact on turnout, we associate precinct-level demographics with the change in turnout between the 2013 gubernatorial and 2014 midterm elections. All else equal, turnout was higher in places where more active registered voters lacked a driver's license. This unexpected relationship might be explained by a targeted Department of Elections mailing, suggesting that the initial impact of voter ID laws may hinge on efforts to notify voters likely to be affected.
Redox-Induced Gating of the Exchange Interactions in a Single Organic Diradical

Embedding a magnetic electroactive molecule in a three-terminal junction allows for the fast and local electric field control of magnetic properties desirable in spintronic devices and quantum gates. Here, we provide an example of this control through the reversible and stable charging of a single all-organic neutral diradical molecule. By means of inelastic electron tunnel spectroscopy we show that the added electron occupies a molecular orbital distinct from those containing the two radical electrons, forming a spin system with three antiferromagnetically coupled spins. Changing the redox state of the molecule therefore switches on and off a parallel exchange path between the two radical spins through the added electron. This electrically controlled gating of the intramolecular magnetic interactions constitutes an essential ingredient of a single-molecule quantum gate.
Multivariate Statistical Methods that Enable Fast Raman Spectroscopy

Rehrauer, Owen G. Ph.D., Purdue University, August 2016. Multivariate Statistical Methods that Enable Fast Raman Spectroscopy. Major Professor: Dor Ben-Amotz. Raman spectroscopy is a useful tool in investigating interand intra-molecular interactions as well as classifying and quantifying chemical species in a sample. Many materials of societal interest, such as proteins and pharmaceuticals, have distinctive Raman spectra with sharp features. However, the adoption of Raman spectra has been hindered by the low rate of Raman scattering, interference from fluorescence, and high spectrometer costs. This work demonstrates multivariate stastical methods that enable fast Raman measurements, despite the low rate of Raman scattering. These methods include a novel type of spectrometer, that uses computer-controlled optical filters to efficiently capture Raman photons and multiplex them onto either one or two photon counting detector(s). This method, referred to as optimal-binary compressive detection (OB-CD), allows for the collection of chemical information in 10’s of microseconds, rather than milliseconds as might be common for Raman spectroscopy performed using a multichannel detector. A method for orthogonalizing moderate amounts of fluorescence from Raman signal in OB-CD is presented. Fast imaging, with speeds as high as 2.5 frames-per-second, is demonstrated and algorithms for image denoising are discussed. Lastly, methods that enables Raman classification using minimal computation time and a technique for accurately processing Raman thermometry data are presented.
Concordance measures in shared frailty models: application to clustered data in cancer prognosis

Frailty models are gaining interest in prognostic studies, especially because of the spread of multicenter studies. However, little research has been performed to extend prognostic tools to frailty models, including discrimination measures. As previously performed for the Harrell's c‐index, we extended two different discrimination measures (the model‐based concordance probability estimation of Gönen and Heller and the nonparametric Uno's c‐index) to take into account cluster membership. We calculate measures at three levels: between‐group, where only patients with different frailties are compared, within‐group, where only patients sharing the same frailty are compared, and overall. We performed simulations to study the impact of group size and the number of groups on these measures. Results showed that the two measures can be extended to frailty models while remaining independent from censoring distribution, provided that the group size is sufficient. We apply the extended measures to two real datasets, a meta‐analysis and a large multicenter trial. Copyright © 2013 John Wiley & Sons, Ltd.
Improving the Accuracy and Efficiency of the k-means Clustering Algorithm

Emergence of modern techniques for scientific data collection has resulted in large scale accumulation of data per- taining to diverse fields. Conventional database querying methods are inadequate to extract useful information from huge data banks. Cluster analysis is one of the major data analysis methods and the k-means clustering algorithm is widely used for many practical applications. But the original k-means algorithm is computationally expensive and the quality of the resulting clusters heavily depends on the selection of initial centroids. Several methods have been proposed in the literature for improving the performance of the k-means clustering algorithm. This paper proposes a method for making the algorithm more effective and efficient, so as to get better clustering with reduced complexity.
DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix

G-quadruplexes, four-stranded structures formed by Guanine-rich nucleic acids, are implicated in many physiological and pathological processes. G-quadruplex-forming sequences are abundant in genomic DNA, and G-quadruplexes have recently been shown to exist in the genome of mammalian cells. However, how G-quadruplexes are formed in the genomes remains largely unclear. Here, we show that G-quadruplex formation can be remotely induced by downstream transcription events that are thousands of base pairs away. The induced G-quadruplexes alter protein recognition and cause transcription termination at the local region. These results suggest that a G-quadruplex-forming sequence can serve as a sensor or receiver to sense remote DNA tracking activity in response to the propagation of mechanical torsion in a DNA double helix. We propose that the G-quadruplex formation may provide a mean for long-range sensing and communication between distal genomic locations to coordinate regulatory transactions in genomic DNA.
Nonadaptive Group Testing With Random Set of Defectives

In a group testing scheme, a series of tests are designed to identify a small number t of defective items that are present among a large number N of items. Each test takes a group of items as input and produces a binary output indicating whether any defective item is present in the group. In a nonadaptive scheme, the tests have to be designed in one-shot. In this setting, designing a testing scheme is equivalent to the construction of a disjunct matrix, an M × N binary matrix where the union of supports of any t columns does not contain the support of any other column. In principle, one wants to have such a matrix with a minimum possible number M of rows. In this paper, we consider the scenario where defective items are random and follow simple probability distributions. In particular, we consider the cases where: 1) each item can be defective independently with probability t/N and 2) each t-set of items can be defective with uniform probability. In both the cases, our aim is to design a testing matrix that successfully identifies the set of defectives with high probability. Both of these models have been studied in the literature before, and it is known that Θ(t log N) tests are necessary as well as sufficient (via random coding) in both the cases. Our main focus is explicit deterministic construction of the test matrices amenable to above scenarios. One of the most popular ways of constructing test matrices relies on constant-weight error-correcting codes and their minimum distance. In particular, it is known that codes result in test matrices with O(t2 log N) rows that identify any t defectives. We go beyond the minimum distance analysis and connect the average distance of a constant weight code to the parameters of the resulting test matrix. Indeed, we show how distance, a pairwise property of the columns of the matrix, translates to a (t + 1)-wise property of the columns. With our relaxed requirements, we show that using explicit constant-weight codes (e.g., based on algebraic geometry codes) we may achieve a number of tests equal to O(t(log2 N/log t)) for both the first and second cases. While only away by a factor of (log N/log t) from the optimal number of tests, this is the best set of parameters that one can obtain from a deterministic construction, and our main contribution lies in relating the group testing properties to the average and minimum distances of constant-weight codes.