Miracle-dz/UniFAR-FTUs huggingface dataset:
Absence of Diauxie during Simultaneous Utilization of Glucose and Xylose by Sulfolobus acidocaldarius

ABSTRACT Sulfolobus acidocaldarius utilizes glucose and xylose as sole carbon sources, but its ability to metabolize these sugars simultaneously is not known. We report the absence of diauxie during growth of S. acidocaldarius on glucose and xylose as co-carbon sources. The presence of glucose did not repress xylose utilization. The organism utilized a mixture of 1 g/liter of each sugar simultaneously with a specific growth rate of 0.079 h−1 and showed no preference for the order in which it utilized each sugar. The organism grew faster on 2 g/liter xylose (0.074 h−1) as the sole carbon source than on an equal amount of glucose (0.022 h−1). When grown on a mixture of the two carbon sources, the growth rate of the organism increased from 0.052 h−1 to 0.085 h−1 as the ratio of xylose to glucose increased from 0.25 to 4. S. acidocaldarius appeared to utilize a mixture of glucose and xylose at a rate roughly proportional to their concentrations in the medium, resulting in complete utilization of both sugars at about the same time. Gene expression in cells grown on xylose alone was very similar to that in cells grown on a mixture of xylose and glucose and substantially different from that in cells grown on glucose alone. The mechanism by which the organism utilized a mixture of sugars has yet to be elucidated.
A Broadband and Electrically Small Planar Monopole Employing Metamaterial Transmission Line

A broadband and electrically small planar monopole is presented in this letter. In order to increase the impedance bandwidth, a metal patch embedded with two epsilon-negative meander lines is used as the main radiator and the ground plane is periodically etched with cross slots. The etched ground and the patch form a metamaterial transmission line (MTL) resonance, which not only miniaturizes the antenna but also improves its bandwidth. The proposed antenna can work in the frequency band of 2.38-2.95 GHz with a fractional bandwidth as much as 21.5%. The size of the main radiator is 0. 078λ0 ×0. 073λ0 and the maximum gain is 3.42 dBi. The antenna can be applied to various wireless mobile communication systems such as RFID, WLAN, and WiFi.
Simulation of Integrated Surface-Water/Ground-Water Flow and Salinity for a Coastal Wetland and Adjacent Estuary

The SWIFT2D surface-water flow and transport code, which solves the St Venant equations in two dimensions, was coupled with the SEAWAT variable-density ground-water code to represent hydrologic processes in coastal wetlands and adjacent estuaries. A sequentially coupled time-lagged approach was implemented, based on a variable-density form of Darcy's Law, to couple the surface and subsurface systems. The integrated code also represents the advective transport of salt mass between the surface and subsurface. The integrated code was applied to the southern Everglades of Florida to quantify flow and salinity patterns and to evaluate effects of hydrologic processes. Model results confirm several important observations about the coastal wetland: (1) the coastal embankment separating the wetland from the estuary is overtopped only during tropical storms, (2) leakage between the surface and subsurface is locally important in the wetland, but submarine ground-water discharge does not contribute large quantities of freshwater to the estuary, and (3) coastal wetland salinities increase to near seawater values during the dry season, and the wetland flushes each year with the onset of the wet season.
Testing for Neutrality in Samples With Sequencing Errors

Many data sets one could use for population genetics contain artifactual sites, i.e., sequencing errors. Here, we first explore the impact of such errors on several common summary statistics, assuming that sequencing errors are mostly singletons. We thus show that in the presence of those errors, estimators of θ can be strongly biased. We further show that even with a moderate number of sequencing errors, neutrality tests based on the frequency spectrum reject neutrality. This implies that analyses of data sets with such errors will systematically lead to wrong inferences of evolutionary scenarios. To avoid to these errors, we propose two new estimators of θ that ignore singletons as well as two new tests Y and Y* that can be used to test neutrality despite sequencing errors. All in all, we show that even though singletons are ignored, these new tests show some power to detect deviations from a standard neutral model. We therefore advise the use of these new tests to strengthen conclusions in suspicious data sets.
The Effects of Moderate- Versus High-Load Resistance Training on Muscle Growth, Body Composition, and Performance in Collegiate Women

Abstract Cholewa, JM, Rossi, FE, MacDonald, C, Hewins, A, Gallo, S, Micenski, A, Norton, L, and Campbell, BI. The effects of moderate- versus high-load resistance training on muscle growth, body composition, and performance in collegiate women. J Strength Cond Res 32(6): 1511–1524, 2018—Twenty young women (20.3 + 1.5 years, 164 + 6 cm, 68.7 + 13.8 kg) without prior structured resistance training experience were recruited for this study. Body composition (BodPod), compartmental water (Bioelectrical Impedance), 7-site skinfold, and arm and thigh cross-sectional area (CSA) were assessed before and after 8-week training. Performance testing consisted of vertical jump, 3-kg chest pass initial velocity, squat 1RM, and overhead press 1RM. After 2 weeks of familiarization training, subjects were matched for body composition and relative squat strength and randomly assigned to either a high-load (HL: n = 10; 4 sets of 5–7 repetitions) or moderate-load (ML: n = 10; 2 sets of 10–14 repetitions) group that completed 6–7 exercises per day performed to momentary muscular failure. Training was divided into 2 lower and one upper body training sessions per week performed on nonconsecutive days for 8 weeks. There were no statistically significant main effects for group or group × time interactions for any variable assessed. Both HL and ML resulted in similar significant increases in lean body mass (1.5 ± 0.83 kg), lean dry mass (1.32 ± 0.62 kg), thigh CSA (6.6 ± 5.6 cm2), vertical jump (2.9 ± 3.2 cm), chest pass velocity (0.334 ± 1.67 m·s−1), back squat one repetition maximum (1RM) (22.5 ± 8.1 kg), and overhead press (3.0 ± 0.8 kg). High-load group and ML group also both resulted in significant decreases in percent body fat (1.3 ± 1.3%), total body water (0.73 ± 0.70 L), and intracellular water (0.43 ± 0.38 L). The results of this study indicate that both moderate-load and high-load training are effective at improving muscle growth, body composition, strength and power in untrained young women.
Renal medullary carcinoma: a case report and brief review of the literature.

BACKGROUND Renal medullary carcinoma (RMC) is an aggressive form of non-clear cell kidney cancer that typically affects young adults and is almost exclusively associated with sickle cell trait. Typical RMC patients tend to be young black males (2:1 male to female predominance) with sickle cell trait who present with pain and hematuria and are found to have metastatic disease at diagnosis. Prognosis is extremely poor, with a mean survival of less than a year in most cases. CASE REPORT We present a case illustrative of many of the classic findings of RMC. A 25-year-old female with a past medical history of sickle cell trait presented to the emergency room with right-sided flank pain. Initially, a computed tomography (CT) scan showed only a benign-appearing cystic lesion 4.5 cm in diameter in the right kidney. Six months later, the patient re-presented with hematuria, lightheadedness, and dizziness. A repeat CT scan showed that the renal cyst had enlarged to 5.6 cm. The patient underwent a decortication and fulguration procedure that revealed malignancy in the wall of the cyst. She was given a series of treatments but experienced progressive disease and passed away 2 years and 8 months after metastatic diagnosis. CONCLUSION Neither systemic therapy nor radiation therapy has been found to be particularly efficacious in the treatment of RMC. As the underlying biologic mechanisms of RMC are further elucidated on a basic science level, we expect new translational research opportunities will emerge and novel treatment options will be developed for this rare and dismal disease.
Clinical Application of a Smartphone-Based Ophthalmic Camera adapter in Under-Resourced Settings in Nepal.

Background The ability to obtain high quality ocular images utilizing smartphone technology is of special interest in under-resourced parts of the world where traditional ocular imaging devices are cost-prohibitive, difficult to transport, and require a trained technician for operation. Purpose The purpose of this study was to explore potential anterior and posterior segment ocular imaging use cases for a smartphone-based ophthalmic camera adapter (Paxos Scope, Digisight Technologies, San Francisco, CA, USA) in under-resourced settings in Nepal. Methods From September to November of 2015 we utilized the Paxos Scope smartphone camera adapter coupled with an iPhone 5 to explore anterior and posterior segment clinical applications for this mobile technology. We used the device at a tertiary eye care facility, a rural eye hospital and a rural cataract outreach camp. We tested the device's capability for high quality photo-documentation in clinic, in the operating room, and in the outreach camp setting. Images were automatically uploaded to a secure, cloud-based electronic medical record system that facilitated sharing of images with other providers for telemedicine purposes. Results Herein we present 17 ocular images documenting a wide variety of anterior and posterior segment pathology using the Paxos Scope from clinical cases seen in a variety of settings in Nepal. Conclusions We found the quality of both the anterior and posterior segment images to be excellent in the clinic, the operating room, and the outreach camp settings. We found the device to be versatile and user-friendly, with a short learning curve. The Paxos Scope smartphone camera adapter may provide an affordable, high-quality, mobile ocular imaging option for under-resourced parts of the world.
Diesel exhaust particles increase LPS‐stimulated COX‐2 expression and PGE2 production in human monocytes

Little is known about health effects of ultrafine particles (UFP) found in ambient air, but much of their action may be on cells of the lung, including cells of the monocyte/macrophage lineage. We have analyzed the effects of diesel exhaust particles (DEP; SRM1650a) on human monocytes in vitro. DEP, on their own, had little effect on cyclooxygenase (COX)‐2 gene expression in the Mono Mac 6 cell line. However, when cells were preincubated with DEP for 1 h, then stimulation with the Toll‐like receptor 4 (TLR4) ligand lipopolysaccharide (LPS) induced an up‐to fourfold‐higher production of COX‐2 mRNA with an average twofold increase. This costimulatory effect of DEP led to enhanced production of COX‐2 protein and to increased release of prostaglandin E2 (PGE2). The effect was specific in that tumor necrosis factor gene expression was not enhanced by DEP costimulation. Furthermore, costimulation with the TLR2 ligand Pam3Cys also led to enhanced COX‐2 mRNA. DEP and LPS showed similar effects on COX‐2 mRNA in primary blood mononuclear cells, in highly purified CD14‐positive monocytes, and in monocyte‐derived macrophages. Our data suggest that UFP such as DEP may exert anti‐inflammatory effects mediated by enhanced PGE2 production.
Benchmarking 6DOF Urban Visual Localization in Changing Conditions

Visual localization enables autonomous vehicles to navigate in their surroundings and augmented reality applications to link virtual to real worlds. Practical visual localization approaches need to be robust to a wide variety of viewing condition, including day-night changes, as well as weather and seasonal variations, while providing highly accurate 6 degree-of-freedom (6DOF) camera pose estimates. In this paper, we introduce the first benchmark datasets specifically designed for analyzing the impact of such factors on visual localization. Using carefully created ground truth poses for query images taken under a wide variety of conditions, we evaluate the impact of various factors on 6DOF camera pose estimation accuracy through extensive experiments with state-of-the-art localization approaches. Based on our results, we draw conclusions about the difficulty of different conditions, showing that long-term localization is far from solved, and propose promising avenues for future work, including sequence-based localization approaches and the need for better local features. We will make our benchmark publicly available.
Modern technology calls for a modern approach to classification of epileptic seizures and the epilepsies

In the last 10–15 years the ILAE Commission on Classification and Terminology has been presenting proposals to modernize the current ILAE Classification of Epileptic Seizures and Epilepsies. These proposals were discussed extensively in a series of articles published recently in Epilepsia and Epilepsy Currents. There is almost universal consensus that the availability of new diagnostic techniques as also of a modern understanding of epilepsy calls for a complete revision of the Classification of Epileptic Seizures and Epilepsies. Unfortunately, however, the Commission is still not prepared to take a bold step ahead and completely revisit our approach to classification of epileptic seizures and epilepsies. In this manuscript we critically analyze the current proposals of the Commission and make suggestions for a classification system that reflects modern diagnostic techniques and our current understanding of epilepsy.
Wechsler Adult Intelligence Scale–Fourth Edition performance in relapsing–remitting multiple sclerosis

Forty patients with relapsing–remitting multiple sclerosis (MS) completed the 10 core Wechsler Adult Intelligence Scale–Fourth Edition (WAIS–IV) subtests. Means for age and education were 42.05 years (SD = 9.94) and 14.33 years (SD = 2.40). For all participants, the native language was English. The mean duration of MS diagnosis was 8.17 years (SD = 7.75), and the mean Expanded Disability Status Scale (EDSS; Kurtzke, 1983) score was 3.73 (SD = 1.41) with a range from 2.0 to 6.5. A control group of healthy individuals with similar demographic characteristics also completed the WAIS–IV and were provided by the test publisher. Compared to controls, patients with MS earned significantly lower subtest and composite scores. The patients' mean scores were consistently in the low-average to average range, and the patterns of performance across groups did not differ significantly, although there was a trend towards higher scores on the Verbal Comprehension Index (VCI) and lower scores on the Processing Speed Index (PSI). Approximately 78% of patients had actual Full Scale IQs that were significantly lower than preillness, demographically based IQ estimates.
Optimization of the performance of an integrated anaerobic-aerobic system for domestic wastewater treatment.

A promising system consisting of Up-flow Anaerobic Sludge Blanket (UASB) and Down-Flow Hanging Sponge (DHS) system was investigated for removal of COD, BOD(5) fractions, ammonia and faecal coliform from domestic wastewater. The combined system was operated at different HRTs of 16, 11 and 8 h. The results indicate that increasing the total HRT from 8 to 16 h significantly (p < 0.05) improves the COD(total) and BOD(5 total) removal mainly as a result of a higher removal of COD(soluble), BOD(soluble), COD(particulate) and BOD(particulate). The main part of coarse suspended solids was removed in the UASB reactor (76.4+/-18%) and the remaining portion was adsorbed and/or enmeshed and degraded in the biomass of the DHS system. The combined system achieved a substantial reduction of total suspended solids (TSS) resulting in an average overall percentage removal of 94+/-6% (HRT = 16 h) and 89.5+/-7.8% (HRT = 8 h). Faecal coliform reduction was significantly improved when increasing the total HRT from 8 to 16 h. Residual counts of faecal coliform were 3.1 x 10(3)/100 ml at a total HRT of 16 h, and 2.8 x 10(4)/100 ml at total HRT of 8 h, corresponding to overall removal efficiency of 99.97+/-0.03 and 99.6+/-0.3% respectively. Despite the increase of ammonia concentration as a result of protein hydrolysis in the UASB reactor, a substantial removal of ammonia was achieved in the DHS system. The results obtained show that decreasing the OLR imposed to DHS system from 2.6 to 1.6 kg COD/m(3). d significantly (p < 0.05) improves the removal efficiency of ammonia by a value of 29%. However, the removal efficiency of ammonia is not further increased when decreasing the OLR from 1.6 to 1.3 kg COD/m(3). d. The discharged sludge from UASB + DHS system exerts a good settling property and partially stabilized.DHS profile results have shown that the major part of COD, BOD(5), and TSS was removed in the upper part of the system, consequently, the nitrification process was occurring in the lower part of the DHS system.
The Jerusalem City-Dump in the Late Second Temple Period

The excavations carried out in recent years by the authors on the eastern slope of the City of David (reich/shukron 2000, 329.337) have encountered, in almost every excavation area, an extremely thick layer of loose debris just under surface. This layer is made of earth, loose rubble, small stones and a large amount of broken artifacts (mainly pottery shards with fragments of stone and glass vessels, coins, etc.), as well as broken animal bones. It seems to be ordinary household garbage, which was dumped down the slope, as is characterized by the slanting bedding lines of the debris. These bedding lines have a constant gradient of approx imately 32 degrees, and they show occasional sorting of the components according to mass and size (Taf. 1). This layer of debris is considerably thick, approximately 6-8m on the average. In our Area C (to the west and to the south of the spring house) it reaches even a thickness of 9 m. Each of the R. weill and Y. shiloh expeditions recorded even 10m (see below). It should be noted that such a phenomenon, dated to the late Second Temple period, is not present on any other side of the immediate outskirts of the city. We may conclude that these deposits contain simple household garbage, of discarded artifacts and waste, and that the area defined above has no connection to any glacis. It simply represents the city-dump. Within the slanting layers of debris no constructions were found. Only in the area close to spring (our Area C), several roughly built terrace-walls were found, built into the loose debris. These terrace-walls were probably the outcome of attempts to stabilize the loose slope, and prevent the debris that was tumbling down, from covering and blocking the outer access to the water. These walls proved useless for this purpose, and were replaced by a stone barrel-shaped vault, built directly above the spring. The inner, westernmost part of this vault, survived to present times. The lowest layers of this debris were found resting directly upon this inner part of vault, thus dating its construction ( reich/Shukron 1999, 60). These thick debris layers were already observed and noted by other scholars who were active on the eastern slope of the City of David prior to our excavations, but little has been elaborated on it.
Dengue virus entry into liver (HepG2) cells is independent of hsp90 and hsp70

Recently, several stress‐related proteins including GRP78, hsp70, and hsp90 have been implicated as dengue virus receptors in various cell types, with hsp90/70 being implicated as a receptor complex in monocytes and macrophages, while GRP78 has been implicated as a liver cell expressed dengue virus receptor. To assess whether the hsp90/70 complex plays a role in the internalization of the dengue viruses into liver cells, we undertook infection inhibition studies with lipopolysaccharide and antibodies directed against both hsp70 and hsp90, individually and in combination. No inhibition of any dengue serotype was seen in the presence of lipopolysaccharide or antibodies directed against either hsp70 or hsp90 either singly or in combination. A moderate inhibition of dengue virus serotype 2 entry into liver cells was observed in the presence of antibodies directed against GRP78. These results confirm a proposed role for GRP78 as a dengue virus serotype 2 receptor protein and suggest that the recently identified hsp90/70 complex does not play a role in dengue virus internalization into liver cells. J. Med. Virol. 79:386–392, 2007. © 2007 Wiley‐Liss, Inc.
Estimation in the Mixture of Markov Chains Moving With Different Speeds

This article considers a new mixture of time-homogeneous finite Markov chains where the mixing is on the rate of movement and develops the EM algorithm for maximum likelihood estimation of the parameters of the mixture. Continuous- and discrete-time versions of the mixture are defined, and their estimation is considered separately. The developed methods are illustrated with an application to modeling bond ratings migration. The class of mixture models proposed in this article provides a framework for modeling population heterogeneity with respect to the rate of movement. The proposed mixture subsumes the mover–stayer model, which has been widely used in applications.
A shift in the ligand responsiveness of thyroid hormone receptor alpha induced by heterodimerization with retinoid X receptor alpha

Thyroid hormone (T3) receptors (T3Rs) are ligand-modulated transcription factors that bind to thyroid hormone response elements (T3REs) and mediate either positive or negative transcriptional regulation of target genes. In addition, in response to ligand binding, T3Rs can interfere with AP-1 activity and thereby inhibit transcription of AP-1-responsive genes. T3Rs were recently shown to form heterodimers with retinoid X receptors (RXRs), leading to increased binding to T3REs in vitro and potentiation of transcriptional responses in vivo. Here we demonstrate that T3R alpha forms stable heterodimers with RXR alpha in living cells. Most important, we describe a new role for RXR alpha in modulating ligand-dependent T3R alpha activity: heterodimerization with RXR alpha greatly increases transcriptional interference with AP-1 activity, augments T3-dependent transcriptional activation, and potentiates the reversal of ligand-independent activation by T3R alpha. In all three cases, the responses occur at substantially lower T3 concentrations when elicited by T3R alpha plus RXR alpha than by T3R alpha alone. In vitro, the binding of T3 decreases the DNA-binding activity of T3R alpha homodimers but does not affect DNA binding by T3R alpha:RXR alpha heterodimers. We provide evidence that increased activities of T3R alpha at lower T3 concentrations are not due to changes in its T3 binding properties. Instead, the altered response could be mediated by either RXR alpha-induced conformational changes, increased stability of heterodimers over homodimers, especially following T3 binding, or both.