Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of CdDHN4, a Novel YSK2-Type Dehydrin Gene from Bermudagrass, Responses to Drought Stress through the ABA-Dependent Signal Pathway

Dehydrin improves plant resistance to many abiotic stresses. In this study, the expression profiles of a dehydrin gene, CdDHN4, were estimated under various stresses and abscisic acid (ABA) treatments in two bermudagrasses (Cynodon dactylon L.): Tifway (drought-tolerant) and C299 (drought-sensitive). The expression of CdDHN4 was up-regulated by high temperatures, low temperatures, drought, salt and ABA. The sensitivity of CdDHN4 to ABA and the expression of CdDHN4 under drought conditions were higher in Tifway than in C299. A 1239-bp fragment, CdDHN4-P, the partial upstream sequence of the CdDHN4 gene, was cloned by genomic walking from Tifway. Bioinformatic analysis showed that the CdDHN4-P sequence possessed features typical of a plant promoter and contained many typical cis elements, including a transcription initiation site, a TATA-box, an ABRE, an MBS, a MYC, an LTRE, a TATC-box and a GT1-motif. Transient expression in tobacco leaves demonstrated that the promoter CdDHN4-P can be activated by ABA, drought and cold. These results indicate that CdDHN4 is regulated by an ABA-dependent signal pathway and that the high sensitivity of CdDHN4 to ABA might be an important mechanism enhancing the drought tolerance of bermudagrass.
Comparing Two Different Approaches in Modeling Small Diameter Energy Wood Drying in Logwood Piles

Moisture management is a key element to improving the cost-efficiency of energy wood supply, through the whole supply chain. Numerous studies of natural drying of forest biomass have been carried out based on traditional sampling of piles or weighing. The latest methodology for monitoring moisture changes has been continuous weighing of biomass in racks built on load cells. The aim of this study was to develop accurate drying models in Austria and Finland for small diameter logs and test the exchangeability of the developed models between countries. Overall drying periods were December 2009 to February 2011 for Austria and March 2012 to June 2013 for Finland. Moisture content dropped from 50.1% to 32.2% (Austria) and from 62.2% to 38.6% (Finland) during the drying periods. Drying performance was evaluated for the period April to October. Two different types of models were developed and the results were cross validated. It proved to be possible to fit satisfactory accurate drying models within the target deviation of ± 5% using both approaches. Whereas the Austrian approach is based on a more basic set of variables, the Finnish approach combines the variables within one. Both ap- proaches are justified depending on the available data.
Fundamental Limits to Position Determination by Concentration Gradients

Position determination in biological systems is often achieved through protein concentration gradients. Measuring the local concentration of such a protein with a spatially varying distribution allows the measurement of position within the system. For these systems to work effectively, position determination must be robust to noise. Here, we calculate fundamental limits to the precision of position determination by concentration gradients due to unavoidable biochemical noise perturbing the gradients. We focus on gradient proteins with first-order reaction kinetics. Systems of this type have been experimentally characterised in both developmental and cell biology settings. For a single gradient we show that, through time-averaging, great precision potentially can be achieved even with very low protein copy numbers. As a second example, we investigate the ability of a system with oppositely directed gradients to find its centre. With this mechanism, positional precision close to the centre improves more slowly with increasing averaging time, and so longer averaging times or higher copy numbers are required for high precision. For both single and double gradients, we demonstrate the existence of optimal length scales for the gradients for which precision is maximized, as well as analyze how precision depends on the size of the concentration-measuring apparatus. These results provide fundamental constraints on the positional precision supplied by concentration gradients in various contexts, including both in developmental biology and also within a single cell.
Cyclin‐dependent kinases as therapeutic targets in melanoma

Decades of scientific insights have led to a recent expansion of the therapeutic menu for melanoma. Despite these advances, the current targeted therapies and immune checkpoint agents continue to yield suboptimal response and cure rates. Hitherto, the most effective targeted therapy strategies have centered on effectors in the mitogen‐activated protein kinase (MAPK) pathway. This review focuses on the emerging evidence of combinatorial approaches targeting both MAPK signaling and dysregulations in cell‐cycle checkpoints. We discuss the prospects and limitations of utilizing strategies that promote cellular senescence, such as inhibition of the interphase cyclin‐dependent kinases (CDKs) and highlight the current state of CDK drug discovery in melanoma.
Impact of value added services on patient waiting time at the ambulatory pharmacy Queen Elizabeth Hospital

Background: Value added services (VAS) are an innovative dispensing system created to provide an alternative means of collecting partial drug supply from our hospital. This in turn was projected to reduce the necessity for patient to visit pharmacy counter and thus reduce the burden of prescription handling. Objective: To evaluate the impact of increased VAS uptake following promotional campaign towards patient waiting time and to explore factors that may affect patient waiting time at the Ambulatory Pharmacy, Queen Elizabeth Hospital. Methods: A quasi experimental study design was conducted from September 2014 till June 2015 at the Ambulatory Pharmacy. During pre-intervention phase, baseline parameters were collected retrospectively. Then, VAS promotional campaign was carried out for six months and whilst this was done, the primary outcome of patient waiting time was measured by percentage of prescription served less than 30 minutes. A linear regression analysis was used to determine the impact of increased VAS uptake towards patient waiting time. Results: An increased in percentage of VAS registration (20.9% vs 35.7%, p<0.001) was observed after the promotional campaign. The mean percentage of prescription served less than 30 minutes increased from 83.2% SD=15.9 to 90.3% SD=11.5, p=0.001. After controlling for covariates, it was found that patient waiting time was affected by number of pharmacy technicians (b=-0.0349, 95%CI-0.0548 : -0.0150, p=0.001), number of pharmacy counters (b=0.1125, 95%CI 0.0631 : 0.1620, p<0.001), number of prescriptions (b=0.0008, 95%CI 0.0004 : 0.0011, p<0.001), and number of refill prescriptions (b=0.0004, 95%CI 0.0002 : 0.0007, p<0.001). The increased in percentage of VAS registration was associated with reduction in number of refill prescription (b=-2.9838, 95%CI -4.2289 : -1.7388, p<0.001). Conclusions: Patient waiting time at the Ambulatory Pharmacy improved with the increased in VAS registration. The impact of increased VAS uptake on patient waiting time resulted from reduction in refill prescriptions. Patient waiting time is influenced by number of pharmacy technicians, number of pharmacy counters, number of prescriptions and number of refill prescriptions.
Venous access: women are equal.

BACKGROUND Arteriovenous fistulae (AVFs) are the preferred method of vascular access for hemodialysis patients; however, the current rate of AVF placement is only 25% to 30% in the United States. This prevalence is even smaller among women and attributed to their perceived inadequate vasculature. This commonly held view that women have less adequate vasculature for AVF placement than men has not been shown objectively in the literature. METHODS To determine a difference in vasculature between the sexes, we retrospectively analyzed data on preoperative vascular mapping in 192 patients. During a 2-year period, vascular mapping of the upper extremities was routinely performed using duplex ultrasound in all patients requiring vascular access in our institution. RESULTS One hundred six of these 192 patients were women, and 86 were men. There was no significant difference in vein size between men and women at any of the sites measured. A total of 87 fistulae were placed in 140 patients, 49% in women and 51% in men (P = 0.16). Prevalences of AVFs were 57% and 68% (P = 0.2) in women and men, respectively. Percentages of fistulae used at the initiation of hemodialysis therapy were 72% in women and 77% in men (P = 0.57). CONCLUSION These data support the view that women have adequate vasculature for the placement of AVFs compared with men. We cannot explain the different outcomes found in other studies; however, we suggest that the differences are caused by physician practice patterns, not anatomic differences between men and women.
Demand Functions in Decision Modeling: A Comprehensive Survey and Research Directions

A variety of mathematical forms have been developed to characterize demand functions which depend on a firm's operational and marketing activities. Such demand functions are being increasingly used by researchers in economics and different functional areas of business. We provide a comprehensive survey of commonly used demand models which depend on (i) price, (ii) rebate, (iii) lead time, (iv) space, (v) quality, and (vi) advertising. Our survey includes single firm–demand models in each category, as well as game theoretic multifirm models involving strategic interaction among the firms. We observe that certain types of functional forms, such as linear, power/iso-elastic, multinomial logit, and multiplicative competitive interaction, have been widely used to construct various demand models in all six categories, but that a large majority of publications deal with categories (i) and (v) of demand models. For each of the six categories, we survey relevant functional forms in the representative papers, and discuss the main properties, the advantages, the disadvantages, and comment on possible future research directions. We also present discussions of the applications of these analytical demand models in empirical studies. The article ends with a summary of our major findings.
Quantity versus quality: the role of layout and interaction complexity in thumbnail-based video retrieval interfaces

In this paper we present our findings from an experiment designed to test the effectiveness of complex, thumbnail based layouts and the interaction methods required, in video retrieval scenarios for handheld devices such as smartphones. Our evaluation explores the relationship between the number of thumbnails (Quantity) visible on screen and their discernible detail (Quality) with regards to the related necessary amount of interaction. The results indicate that such layouts achieve a very high rate of accuracy and speed but that the nature of the interaction is of critical importance for the success of the system.
Cyclooxygenase Inhibitors as a New Therapeutic Strategy in Small Bowel Transplantation

Background The long-term outcome of intestinal transplantations is still not favorable, which is partly due to the intestinal susceptibility to ischemia. There are several indications that the inflammatory response to ischemia-reperfusion injury is mediated by cyclooxygenases and that their inhibition may be associated with improved organ function. The aim of this study was to analyze if cyclooxygenase (COX) inhibitors could improve the early posttransplant outcome after orthotopic small bowel transplantation. Methods Small bowel transplantation was performed between rats to test the impact of nonselective (Piroxicam), preferential (Meloxicam), and selective COX-2 inhibitors (Parecoxib). The donor intestines were either perfused and stored with inhibitor or had inhibitor administered intravenously after transplantation. Results Using COX inhibitors, a sequential increase of posttransplantation intestinal integrity could be shown, with Parecoxib the least effective and Meloxicam the most effective treatment. These differences were in line with the downregulation of COX-2 activity by the inhibitors. Functionally, the same tendency could be seen in diminished expression of proinflammatory molecules, decreased leucocyte inflammation, and significantly improved graft microcirculation. In most cases, the intravenous administration was more effective. However, the COX inhibitors used were shown to cause relevant hepatotoxicity under nearly all conditions, but particularly under intravenous administration. Only Meloxicam in histidine-tryptophan-ketoglutarate was demonstrated to be a safe drug without hepatotoxic side effects. Conclusions The activity of COX contributes to ischemia-reperfusion injury after intestinal transplantation. In this comparative study, the administration of the preferential COX-2 inhibitor Meloxicam via histidine-tryptophan-ketoglutarate showed the best graft-protective attributes and the lowest hepatotoxic side effects.
Massive programmed translational jumping in mitochondria

Significance During translation, ribosomes decode mRNAs in a sequential fashion. In this paper, we report the discovery of more than 80 translational bypassing elements (byps) 27–55 nt long in mitochondrial protein-coding regions of the yeast Magnusiomyces capitatus. We demonstrate experimentally that byps are retained in mRNA but not translated into protein. Byps somewhat resemble the single bypass element in bacteriophage T4 but also display unique features. We further discovered byp-like sequences in other yeast species, indicating that these inserts are mobile genetic elements. In contrast to byps, byp-like sequences are not bypassed during translation. When inserted in variable protein regions, they have the potential to drive the evolutionary diversification of protein structure and function. Programmed translational bypassing is a process whereby ribosomes “ignore” a substantial interval of mRNA sequence. Although discovered 25 y ago, the only experimentally confirmed example of this puzzling phenomenon is expression of the bacteriophage T4 gene 60. Bypassing requires translational blockage at a “takeoff codon” immediately upstream of a stop codon followed by a hairpin, which causes peptidyl-tRNA dissociation and reassociation with a matching “landing triplet” 50 nt downstream, where translation resumes. Here, we report 81 translational bypassing elements (byps) in mitochondria of the yeast Magnusiomyces capitatus and demonstrate in three cases, by transcript analysis and proteomics, that byps are retained in mitochondrial mRNAs but not translated. Although mitochondrial byps resemble the bypass sequence in the T4 gene 60, they utilize unused codons instead of stops for translational blockage and have relaxed matching rules for takeoff/landing sites. We detected byp-like sequences also in mtDNAs of several Saccharomycetales, indicating that byps are mobile genetic elements. These byp-like sequences lack bypassing activity and are tolerated when inserted in-frame in variable protein regions. We hypothesize that byp-like elements have the potential to contribute to evolutionary diversification of proteins by adding new domains that allow exploration of new structures and functions.
Aspects of favorable propagation in Massive MIMO

Favorable propagation, defined as mutual orthogonality among the vector-valued channels to the terminals, is one of the key properties of the radio channel that is exploited in Massive MIMO. However, there has been little work that studies this topic in detail. In this paper, we first show that favorable propagation offers the most desirable scenario in terms of maximizing the sum-capacity. One useful proxy for whether propagation is favorable or not is the channel condition number. However, this proxy is not good for the case where the norms of the channel vectors are not equal. For this case, to evaluate how favorable the propagation offered by the channel is, we propose a “distance from favorable propagation” measure, which is the gap between the sum-capacity and the maximum capacity obtained under favorable propagation. Secondly, we examine how favorable the channels can be for two extreme scenarios: i.i. d. Rayleigh fading and uniform random line-of-sight (UR-LoS). Both environments offer (nearly) favorable propagation. Furthermore, to analyze the UR-LoS model, we propose an urns-and-balls model. This model is simple and explains the singular value spread characteristic of the UR-LoS model well.
UCSD Performance-Based Skills Assessment

Instruments to assess everyday functioning have utilized self-report, proxy report, clinician ratings, or direct observation of performance. Each of these methods has strengths and weaknesses. In this article we argue for the inclusion of performance-based measures of functional capacity in studies of severely mentally ill persons and describe a new measure, the UCSD Performance-Based Skills Assessment (UPSA). We administered the UPSA to 50 middle-aged and older outpatients with schizophrenia or schizoaffective disorder, and 20 normal comparison subjects. Participants' performance in five domains of functioning (Household Chores; Communication; Finance; Transportation; and Planning Recreational Activities) was assessed in standardized role-play situations. Administration of the UPSA required an average of 30 minutes to complete. Interrater reliability of ratings was excellent Patients' performance was significantly more impaired than that of normal subjects. Among patients, the UPSA performance correlated significantly with severity of negative symptoms and of cognitive impairment but not with that of positive or depressive symptoms. The UPSA scores correlated highly with those on another performance-based measure. We believe that UPSA would be useful for assessing everyday functioning in severely mentally ill adults.
Sources of Long‐Range Anthropogenic Noise in Southern California and Implications for Tectonic Tremor Detection

We study anthropogenic noise sources seen on seismic recordings along the central section of the San Jacinto fault near Anza, southern California. The strongest signals are caused by freight trains passing through the Coachella Valley north of Anza. Train-induced transients are observed at distances of up to 50 km from the railway, with durations of up to 20 min, and spectra that are peaked between 3 and 5 Hz. Additionally, truck traffic through the Coachella Valley generates a sustained hum with a similar spectral signature as the train transients but with lower amplitude. We also find that wind turbine activity in northern Baja California introduces a seasonal modulation of 1– to 5-Hz energy across the Anza network. We show that the observed train-generated transients can be used to constrain shallow attenuation structure at Anza. Using the results from this study as well as available borehole data, we further evaluate the performance of approaches that have been used to detect nonvolcanic tremor at Anza. We conclude that signals previously identified as spontaneous tremor (Hutchison and Ghosh, 2017) were probably generated by other nontectonic sources such as trains. Electronic Supplement: Seismograms during a transient, decomposition of the large amplitude signal into sequences of repeating patterns, detection statistics in the two stages of the tremor search procedure, velocity amplitude spectra of transients from two collocated borehole–surface station pairs, median weekday–night spectra for all stations in the Plate Boundary Observatory (PBO) Anza network, time variations of root mean square (rms) velocity for all stations in the PBO Anza network, cumulative population and kilometers of railroad on which the allowed speed for freight trains exceeds 50 mph, envelopes of vertical ground motions as a function of time, vertical ground motions recorded by the Anza borehole stations, and spectrograms of vertical ground motion and corresponding wind speeds.
High XRCC1 Protein Expression Is Associated with Poorer Survival in Patients with Head and Neck Squamous Cell Carcinoma

Purpose: We evaluated X-ray repair complementing defective repair in Chinese hamster cells 1 (XRCC1) protein in head and neck squamous cell carcinoma (HNSCC) patients in association with outcome. Experimental Design: XRCC1 protein expression was assessed by immunohistochemical (IHC) staining of pretreatment tissue samples in 138 consecutive HNSCC patients treated with surgery (n = 31), radiation (15), surgery and radiation (23), surgery and adjuvant chemoradiation (17), primary chemoradiation (51), and palliative measures (1). Results: Patients with high XRCC1 expression by IHC (n = 77) compared with patients with low XRCC1 expression (n = 60) had poorer median overall survival (OS; 41.0 months vs. OS not reached, P = 0.009) and poorer progression-free survival (28.0 months vs. 73.0 months, P = 0.031). This association was primarily due to patients who received chemoradiation (median OS of high- and low-XRCC1 expression patients, 35.5 months and not reached respectively, HR 3.48; 95% CI: 1.44–8.38; P = 0.006). In patients treated with nonchemoradiation modalities, there was no survival difference by XRCC1 expression. In multivariable analysis, high XRCC1 expression and p16INK4a-positive status were independently associated with survival in the overall study population (HR = 2.62; 95% CI: 1.52–4.52; P < 0.001 and HR = 0.21; 95% CI: 0.06–0.71; P = 0.012, respectively) and among chemoradiation patients (HR = 6.02; 95% CI: 2.36–15.37; P < 0.001 and HR = 0.26; 95% CI: 0.08–0.92, respectively; P = 0.037). Conclusions: In HNSCC, high XRCC1 protein expression is associated with poorer survival, particularly in patients receiving chemoradiation. Future validation of these findings may enable identification of HNSCC expressing patients who benefit from chemoradiation treatment. Clin Cancer Res; 17(20); 6542–52. ©2011 AACR.
Architectural impact of secure socket layer on Internet servers

Secure socket layer (SSL) is the most popular protocol used in the Internet for facilitating secure communications. In this paper, we analyze the performance and architectural impact of SSL on the servers in terms of various parameters such as throughput, utilization, cache sizes, cache miss ratios, number of processors, control dependencies, file access sizes, bus transactions, network load, etc. The major conclusions from this study are as follows: The use of SSL increases computational cost of the transactions by a factor of 5-7. SSL transactions do not benefit much from a larger L2 cache, but a larger LI cache would be helpful. A complex logic for handling control dependencies is not useful for SSL transaction as the frequency of branches is very low. Because SSL workload is highly CPU bound, it may be possible to enhance SSL performance by using a number of other architectural features as well.