Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence that ion conduction in 5-HT3A receptors proceeds through lateral portals in the cytosol

The intracellular domain of the serotonin type 3A receptor, a pentameric ligand-gated ion channel, is crucial for regulating conductance. However, the specific ion conduction pathway through this domain is less clear. The intracellular domain starts with a short loop after the third transmembrane segment, followed by a short α-helical segment, a large unstructured loop, and finally the membrane-associated MA-helix that continues into the last transmembrane segment. The MA-helices from all five subunits form the extension of the transmembrane ion channel and shape what has been described as a “closed vestibule”, with their lateral portals obstructed by loops and their cytosolic ends forming a tight hydrophobic constriction. The question remains whether the lateral portals or cytosolic constriction conduct ions upon channel opening. In the present study, we used disulfide bond formation between pairs of engineered cysteines to probe the proximity and mobility of segments of the MA-helices most distal to the membrane bilayer. Our results indicate that the proximity and orientation for cysteine pairs at I409C/R410C, in close proximity to the lateral windows, and L402C/L403C, at the cytosolic ends of the MA-helices, are conducive for disulfide bond formation. While conformational changes associated with gating promote crosslinking for I409C/R410C, which in turn decreases channel currents, crosslinking of L402C/L403C is functionally silent in macroscopic currents. These results support the hypothesis that concerted conformational changes open the lateral portals for ion conduction, rendering ion conduction through the vertical portal unlikely. Significance The intracellular domain (ICD) of pentameric ligand-gated ion channels (pLGICs) is the most diverse domain within receptors of the Cys-loop superfamily. Despite being the least understood domain of pLGICs, its impact on ion-channel function and contribution to the cytosolic exit pathway of the channel have been investigated. X-ray and cryo-EM structures have captured the structured segments of the ICD of 5-HT3A receptors in different conformational states with lower resolution of the ICD as compared to the other domains. Here, we provide experimentally derived evidence for the importance of the differential mobility of the cytosolic segment of the MA-helices, which supports the existence of lateral portals as opposed to a vertical pathway for 5-HT3A receptors.
Diversification of mammalian deltaviruses by host shifting

Significance Satellites are virus-like agents which require both a host and a virus to complete their life cycle. The only human-infecting satellite is hepatitis delta virus (HDV), which exacerbates liver disease in patients co-infected with hepatitis B virus (HBV). How HDV originated is a long-standing evolutionary puzzle. Using terabase-scale data mining, coevolutionary analyses, and field studies in bats, we show that deltaviruses can jump between highly divergent host species. Our results further suggest that the contemporary association between HDV and HBV likely arose following zoonotic transmission from a yet-undiscovered animal reservoir in the Americas. Plastic host and virus associations open prospects that deltaviruses might alter the virulence of multiple viruses in multiple host species. Hepatitis delta virus (HDV) is an unusual RNA agent that replicates using host machinery but exploits hepatitis B virus (HBV) to mobilize its spread within and between hosts. In doing so, HDV enhances the virulence of HBV. How this seemingly improbable hyperparasitic lifestyle emerged is unknown, but it underpins the likelihood that HDV and related deltaviruses may alter other host–virus interactions. Here, we show that deltaviruses diversify by transmitting between mammalian species. Among 96,695 RNA sequence datasets, deltaviruses infected bats, rodents, and an artiodactyl from the Americas but were absent from geographically overrepresented Old World representatives of each mammalian order, suggesting a relatively recent diversification within the Americas. Consistent with diversification by host shifting, both bat and rodent-infecting deltaviruses were paraphyletic, and coevolutionary modeling rejected cospeciation with mammalian hosts. In addition, a 2-y field study showed common vampire bats in Peru were infected by two divergent deltaviruses, indicating multiple introductions to a single host species. One vampire bat-associated deltavirus was detected in the saliva of up to 35% of individuals, formed phylogeographically compartmentalized clades, and infected a sympatric bat, illustrating horizontal transmission within and between species on ecological timescales. Consistent absence of HBV-like viruses in two deltavirus-infected bat species indicated acquisitions of novel viral associations during the divergence of bat and human-infecting deltaviruses. Our analyses support an American zoonotic origin of HDV and reveal prospects for future cross-species emergence of deltaviruses. Given their peculiar life history, deltavirus host shifts will have different constraints and disease outcomes compared to ordinary animal pathogens.
Laboratory-Scale Investigation of the Effect of Microbial Growth on the Geoelectrical Properties of Porous Media

We investigated the effect of microbial growth and biofilm formation on low-frequency complex conductivity in porous media. Understanding the direct contribution of microbial growth to the lowfrequency electrical response of porous media will lead to the development of models necessary for the interpretation of geoelectrical data from near-surface microbial-active geologic media (e.g. bioremediation). The objectives of this study were to determine (1) the direct effect of microbial growth and biofilm formation, and (2) the relative magnitude of the effect of microbial growth and biofilm formation on low-frequency complex conductivity of porous media. Silica sand packed columns (one control and one experimental set) were constructed in triplicate, treated with nutrient broth and diesel fuel, and microbial growth was stimulated in the experimental columns by the addition of a mixed bacteria culture. Low frequency (0.1-1000 Hz) electrical measurements, and geochemical analyses (i.e. pH, fluid conductivity) were made twice a week for the 60 day duration of the experiment. Sand was periodically sampled from the columns for microbial analysis (extraction of microbial cells from sand grains for direct microbial counting) and environmental scanning electron microscope (ESEM) imaging of grain surface characteristics. The experimental (biostimulated) columns showed a peak in the imaginary conductivity measurements on day 23 (maximum ~8 x 10 S/m) which corresponded with a peak in the microbial cell concentrations (~7 x 10 cells/mL), followed by a sharp decrease in both the imaginary conductivity and microbial concentrations. The real conductivity showed a general, relatively small increase (<0.04 S/m) between day 0 and 34 for both the control and experimental columns, before decreasing slightly (~0.01 S/m). The close correspondence of the peaks in the imaginary conductivity and microbial cell concentrations in the experimental column suggest that microbial growth in porous media effects the imaginary (interfacial) conductivity to a greater degree than the real (electrolytic) conductivity, which did not appear to show a relationship with the microbial cell concentrations. We conclude from this study that low-frequency electrical measurements (imaginary conductivity) may aid in investigations aimed at assessing the rate of microbial growth and biofilm formation in porous media.
Associação entre incidência de dengue e variáveis climáticas Association between dengue incidence and climatic factors

ABSTRACT OBJECTIVE : To describe the occurrence of autochthonous dengue cases accordingto sex, age, suspected infection site and its relation with climatic variables. METHODS : Autochthonous dengue cases reported in Sao Sebastiao, SouthernBrazil, from 2001 to 2002 and confirmed in laboratory were studied. Larval densitywas verified by three indexes: building, recipients and Breteau. The relationshipbetween rainfall, temperature and number of cases was analyzed through Spearman’scorrelation using time lag. RESULTS : The annual incidence coefficients for 2001 and 2002 were 80.3 and211.1 per 10,000 inhabitants, respectively. Most dengue cases (n=1,091; 65%) werereported in the district’s central area. Females (n=969; 60%) and the age groups 20 to Andressa F Ribeiro I Gisela R A M Marques I Julio C Voltolini II Maria Lucia F Condino I I Superintendencia de Controle deEndemias. Sao Paulo, SP, Brasil I I Departamento de Ciencias Biologicas.Universidade de Taubate. Taubate, SP,Brasil Correspondencia | Correspondence:
Complementary Alternative Therapies: Green Tea Flavonoids in Acne Vulgaris

ABSTRACT Drugs are medications or substances that are used to modify physiologic responses and alleviate associated symptoms. In dermatology, medications and substances are utilized on a daily basis and include topical treatments to anesthetics in micrographic surgery to biologic-acting immunologic agents. The purposes of this section are to focus on drug, specifically how it works and how it is utilized, and to discuss routine alternatives (if available). In this column, we will focus on the uses, mechanism of action, and adverse effects of green tea in acne vulgaris.
Clinical and experimental investigation: relationship of ischaemia/reperfusion injury with oxidative stress in abdominal aortic aneurysm repair and in extracranial brain artery endarterectomy and possibilities of protection against ischaemia using a glutathione analogue in a rat model of global brai

Background and Aims: During elective abdominal aortic aneurysm repair (AAAR), low­ er torso ischaemia-reperfusion event is unavoidable. Previous studies on AAAR have reported the importance of oxidative stress (OS) in ischaemia-reperfusion injury, how­ ever, the grade of OS has not been adequately clarified up to now. The aim of this study was to perform a complex investigation of the time-course and grade of systemic and cellular OS in patients undergoing AAAR. Material and Methods: Arterial blood samples were taken from 18 patients undergo­ ing elective AAAR (at four points in time: before anaesthesia, 5 min after aortic clamp­ ing and 5 min and 30 min after clamp removal). Diene conjugates (DC), thiobarbituric acid reactive substances (TBARS), total antioxidative capacity (TAC), glutathione redox ratio (GSSG/GSH), and levels o f antioxidative enzymes as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSHPx) were measured from the radial ar­ terial blood. Results: 30 min after the removal of the aortic cross-clamp, arterial CAT showed sig­ nificant elevation (96.0 vs 56.9 U/l, p < 0.05); GSHPx was significantly elevated (51.5 vs 39.9 U/g Hgb, p < 0.05) and TAC was decreased (31.4 vs 36.5 %, p < 0.05) in comparison with preoperative value. Conclusions: We found limited alterations of several OS parameters, which do not characterize either systemic or cellular high-grade OS during elective AAAR.
Hiperproteicas diets and metabolic consequences

High protein intake produces an increase in net acid excretion, which in turn leads to an increase in urinary calcium. Effects of diet in urinary acid and calcium excretion depend not only on the protein content, but also may be modified by other constituents such as potassium and alkali equivalents of bicarbonate present in fruits and vegetables. Diets deficient in these potassium bases increase the acid load imposed by proteins. In consequence, diets with a high protein intake or poor in fruits and vegetables produce a low-grade systemic metabolic acidosis which exerts deleterious effects on the body, including growth retardation in children, decreased muscle and bone mass in adults, and kidney stone formation. This review intends to summarize the present evidence in relation to the effects of high protein diets in different organs and systems including hydroelectrolytic and acid base metabolism, bone metabolism, renal and endocrine function. Particular aspects that may exert a special influence in life extremes as childhood and old age are also addressed. An Venez Nutr 2009;22 (2): 95-104.
Covering Kids & Families Evaluation: Expectations of Sustainability: What Do CKF Grantees and State Officials Predict Will Happen Once RWJF Funding Ends?

The Covering Kids and Families (CKF) program was designed to develop and launch state and local coalitions that would work to expand public health insurance coverage of the uninsured. The Foundation intended, once these coalitions were launched, to begin reducing its funding, with the eventual goal of having the coalitions fund themselves entirely from local support. Beginning in January 2006, the Foundation will indeed begin to phase out its funding for the 46 CKF state grantees. But what will happen in this post-grant period? Will CKF grantees find other sources of support and continue to operate? Or will they disappear or shift their goals? To find out what the grantees, and the state officials who have worked with them, predict will happen, the evaluation team surveyed them in July 2005. The survey found that most grantees, and a majority of state Medicaid and SCHIP officials, are optimistic that the CKF projects in their states can continue at least some activities after funding ends. Both groups believe it is likely that the current grantee, in some instances with other organizations, will be able to continue activities. Indeed, 16 of the 46 state grantees have secured continued funding from other sources. However, as of summer 2005, most grantees—including those whose grants end soonest, in early 2006—had not yet secured funding for the future, which has raised concerns that activities will not be sustained in many states.
ALPHA FACTORS IN FULL-SCALE WASTEWATER AERATION SYSTEMS

Surface active agents depress gas transfer at gas-liquid interfaces. They are present as measurable trace contaminants at all environmental and at most industrial gas-liquid interfaces. This paper presents the results of several studies, including lab and full scale studies that show the depression of gas transfer, usually quantified by the alpha factor, can be related to the Reynolds number and the level of wastewater treatment. Our results offer a tool for mass transfer prediction from flow regime and dynamic surface tension properties.
Strong reciprocity and the welfare state

We explore the contribution of reciprocity and other non selfish motives to the political viability of the modern welfare state. In the advanced economies, a substantial fraction of total income is regularly transferred from the better off to the less well off, with the approval of the electorate. Economists have for the most part misunderstood this process due to their endorsement of an empirically implausible theory of selfish human motivation. Drawing on anthropological, experimental, public opinion survey and other data we develop an alternative behavioral explanation for economic reasoning about sharing and insurance. In this alternative view, reciprocity motives are necessary for understanding support for and opposition to the welfare state. Modern citizens willingly share with those who uphold societal norms about what constitutes morally worthy behavior, while frequently seeking to punish those who transgress those norms, even when these actions are individually costly and yield no individual material benefit.
Single-particle entanglement

I give a simple argument that demonstrates that the state vertical bar 0> vertical bar 1>+ vertical bar 1> vertical bar 0>, with |0> denoting a state with 0 particles (or photons) and vertical bar 1> a one-particle state, is entangled in spite of recent claims to the contrary. I also discuss viewpoints on the old controversy about whether the above state can be said to display single-particle or single-photon nonlocality.
A NOVEL DE-INTERLACE BASED ON SPATIO-TEMPORAL WEIGHT ADAPTIVE AND EDGE-DIRECTED INTERPOLATION

De-interlace is an image format conversion from interlaced image to progressive one. In this paper, a de-interlacing algorithm based on spatio-temporal weight and edge direction is presented. It consists of motion detection, low-angle edge detection, spatio-temporal weight calculation, and adaptive interpolation. Same-parity fields motion estimation is adopted to improve the accuracy of motion estimation. And edge direction adaptive interpolation is proposed to sharpen edges and remove the saw-tooth artifacts in which the minimum 6deg edge can be detected. Experimental results show that the proposed method achieves high image quality and low hardware complexity
NEW DEVELOPMENTS TOWARD NON-CONTACTING SEISMICS

Buried landmines and chemical waste may provide the contrast in elastic properties within soil needed to achieve detection via near-surface seismic methods. The hazardous nature of these targets strongly indicates the need for non-contacting sources and receivers. An ultrasonic parametric array allows us to insonify the soil with an intense focused beam of sound; this acoustic energy is converted to elastic waves in soil. Our non-contacting seismometer is a microwave Doppler vibrometer that can detect seismic waves, even through foliage. We believe that developments along these lines will ultimately lead to the ability to probe large areas of the near-surface with elastic waves in a safe and reliable fashion, without physically touching the ground. This is a report on some of the new developments in building a non-contacting seismic data acquisition system. Introduction Landmines and unexploded ordinance (UXO) are a sizable hazard in many places in the world. It is estimated that about 70 million landmines are spread throughout 70 countries. About 26, 000 people are killed each year due to landmines and UXO (Perera, 2003). Many techniques are being investigated to detect landmines accurately, safely and rapidly. The combination of these requirements poses a formidable technical challenge. All methods to detect landmines rely on a contrast of some physical property between the landmine and the surrounding soil. Some of these methods are not sensitive enough, some are too sensitive, causing many false alarms; current methods investigate over 300 false alarms for every mine found. Also, most of these methods require contact with the surface, which increases the risk of accidental detonation. We are investigating the feasibility of fully non-contacting landmine detection based on a novel combination of microwave and nonlinear acoustic methods. Such a non-contacting seismic data acquisition system could prove extremely useful for problems besides detecting buried landmines (Donskoy et al., 2002; Xiang & Sabatier, 2003), such as hazardous waste monitoring (Kaduchak et al., 2000), monitoring of buried infrastructure (Buyukozturk, 1997; Pla-Rucki & Eberhard, 1995), monitoring structural integrity, and other near surface geophysical applications. Some of the possible benefits of this non-contacting system over conventional (contacting) seismology include the • safety of remote sensing. • ability to scan the surface with both source and receiver, thereby measuring spatial waveforms.
New Record of Odontobutis potamophila in Tarim River,China

收稿日期: 2009 02 20,修回日期: 2009 04 23 2006年 10月 28 日, 作者在新疆阿拉尔市 塔里木大学集贸市场采购到 1尾活的属于塘鳢 科小鱼; 2007年 6月 15日, 塔里木大学文理学 院学生在新疆生产建设兵团农一师十二团八连 (属阿拉尔市管辖)塔里木河灌溉沟渠中抓获一 批小杂鱼,从中获得 6尾与上述小鱼同样的鱼; 2008年6月,塔里木大学动物科学学院水产养 殖专业学生在农一师十四团附近塔里木河灌溉 沟渠进行课程实习时, 采集的鳅科鱼类中也混 有不少这样的鱼。 经鉴定,该批塘鳢科鱼为河 川沙塘鳢( Odontobutis potamophila G. nther) , 属 鲈形目 ( Perciformes) 塘鳢科 ( Eletridae )沙塘鳢 属。 标本现保存于塔里木大学动物科学学院鱼 类学标本室。 对采集的标本描述如下。 鉴定依 中国鱼类系统检索 [ 1] 及伍汉霖 等 [ 2] ,描述标本2尾。 主要形态特征 体延长, 前部圆筒形,后部 侧扁。 头大,平扁。 体被栉鳞, 头部被小圆鳞。 颌齿细小, 多行。 背鳍 2 个, 腹鳍分离, 不成吸 盘状,尾鳍圆形。 眼后方有感觉管孔,眼前下方 横行感觉乳突线的端部乳突排列呈直线状, 眼 后下方横行感觉乳突线与眼下纵行感觉乳突线 相连。 其中两尾可数性状为: 背鳍 ! , ∀ 10; 胸鳍 15; 腹鳍∀ 5; 臀鳍∀ 8,纵列鳞 35。 可量 性状如下(单位: mm) :
Restriction mapping of Cucurbitae pepo L. chloroplast DNA Pstl 9.8 kb fragment and detection of ORF 2280 transcripts

Using tomato heterologous probe, the ORF 2280 was located on the PstI 9.8 kb fragment in the inverted repeat A (IRA) and on the PstI 12.1 kb fragment in the inverted repeat B (IRB) on the physical map of squash chloroplast DNA. A fine map of the PstI 9.8 kb fragment was developed using SalI, BamHI and EcoRI restriction enzymes.Two transcripts of 1.4and 2.6 kbs of ORF 2280 of squash plastid DNA were detected in fruits but not in the leaves of Early Prolific cultivar using a heterologous PstI 1.2 kb tomato plastid DNA probe internal to ORF 2280.In Bicolor gourd fruits, 1.4 and 2.6 kb transcripts of ORF 2280 weredetected both in the fruits and in leaves. Key Words: Cucurbitae pepo, restriction mapping, PstI 9.8 kb fragment, ORF 2280 transcripts. African Journal of Biotechnology Vol.4(1) 2005: 1-8
Effects of Calcium and Auxin on Russet Spotting and Phenylalanine Ammonia-lyase Activity in Iceberg Lettuce

In the article “Effects of Calcium and Auxin on Russet Spotting and Phenylalanine Ammonialyase Activity in Iceberg Lettuce” by Dangyang Ke and Mikal E. Saltveit, Jr. (HortScience 21:1169–1171, Oct. 1986), Dangyang Ke's name was spelled incorrectly.
A NEW JOINT INVERSION APPROACH APPLIED TO THE COMBINED TOMOGRAPHY OF DC RESISTIVITY AND SEISMIC REFRACTION DATA

We present a new joint inversion approach that allows for a combined inversion of independent physical parameters by exchanging structural information. The technique is based on the ideas of robust modeling. Occurring gradients of one parameter facilitate the development of gradients in the other but does not enforce this. In the presence of boundaries that can be seen by both methods it leads to sharp contrasted models. Finally, a combined image of the subsurface is obtained by cluster analysis. The technique is applied to the inversion of dc resistivity and seismic refraction data. Two synthetic data sets show how different boundary types are resolved with and without structural coupling. It is demonstrated how the quality of the inversion results is improved by the new approach. Introduction The joint interpretation of different measurement types is a basic principle to confine the ambiguity of the inverse problems in geophysics. In the existing approaches one inverts for one parameter using an augmented data vector (Vozoff and Jupp, 1975). This is only possible if all measurements depend on the same parameter or if the parameters are interconnected by some petrophysical relationship. However, often such a relationship does not exist, as for electrical conductivity and seismic velocity. Nevertheless, we expect at least similar structures in the resulting models. Therefore we like to combine the otherwise independent inversions to allow for structural similarities. The challenge is to facilitate similar structures without enforcing it. Gallardo and Meju (2004) presented an algorithm where a combined data functional based on the cross-gradients of both models is minimized. However, one problem is the weighting of the individual data and model updates for different data numbers and convergence properties. Here we present an approach where two inversion runs are carried out separately. The combination of both models is accomplished by mutually controlled structural weights based on the principles of robust modeling. First we describe the minimization problem and the regularization procedure. Thereafter we introduce robust modeling and depict how structural information may be interchanged. We apply this technique to the dc resistivity and seismic refraction data on unstructured meshes. Two synthetic models using different model boundaries shows how the joint inversion improves the model concept. Inversion Minimization procedure Assume D data points di subsumed in a data vector d = (d1, . . . , dD). The parameter distribution p(~r) is discretized byM basis functions ψj and their coefficientsmj ,