Miracle-dz/UniFAR-FTUs huggingface dataset:
mRNA 3’ of the A Site Bound Codon is Located Close to Protein S3 on the Human 80S Ribosome

Ribosomal proteins neighboring the mRNA downstream of the codon bound at the decoding site of human 80S ribosomes were identified using three sets of mRNA analogues that contained a UUU triplet at the 5’ terminus and a perfluorophenylazide cross-linker at guanosine, adenosine or uridine residues placed at various locations 3’ of this triplet. The positions of modified mRNA nucleotides on the ribosome were governed by tRNAPhe cognate to the UUU triplet targeted to the P site. Upon mild UV-irradiation, the mRNA analogues cross-linked preferentially to the 40S subunit, to the proteins and to a lesser extent to the 18S rRNA. Cross-linked nucleotides of 18S rRNA were identified previously. In the present study, it is shown that among the proteins the main target for cross-linking with all the mRNA analogues tested was protein S3 (homologous to prokaryotic S3, S3p); minor cross-linking to protein S2 (S5p) was also detected. Both proteins cross-linked to mRNA analogues in the ternary complexes as well as in the binary complexes (without tRNA). In the ternary complexes protein S15 (S19p) also cross-linked, the yield of the cross-link decreased significantly when the modified nucleotide moved from position +5 to position +12 with respect to the first nucleotide of the P site bound codon. In several ternary complexes minor cross-linking to protein S30 was likewise detected. The results of this study indicate that S3 is a key protein at the mRNA binding site neighboring mRNA downstream of the codon at the decoding site in the human ribosome.
Juvenile hormone mediates a trade‐off between primary and secondary sexual traits in stalk‐eyed flies

SUMMARY Trade‐offs between developing body parts may contribute to variation in allometric scaling relationships in a variety of taxa. Experimental evidence indicates that both circulating levels of juvenile hormone (JH) and sensitivities of developing body parts to JH can influence morphology in polyphenic insects. However, the extent to which JH may regulate both the development of traits that scale continuously with body size and trade‐offs between these traits is largely unknown. Here, I present evidence that the JH analog methoprene applied to final instar larvae of a stalk‐eyed fly (Cyrtodiopsis dalmanni) can induce males to produce larger eye‐stalks relative to their body size. Examination of testis growth, sperm transfer, and egg maturation indicates that JH induces a trade‐off between eye‐span and gonad development in adult males, but not females. Age at sexual maturity was unaffected by larval JH applications to either sex. Collectively, these results are consistent with JH‐mediated allocation of resources to eye‐span at the expense of testes, and indicate potential costs for the production of an exaggerated trait.
Why do homogeneous firms export dierently? A density externality approach of trade. preliminary and incomplete

While it is now well understood why the average exporting firm has a higher productivity than a pure domestic firm, the theoretical literature has remained silent on why firms do not enter foreign markets according to an exact hierarchy as predicted by models a la Melitz. To this aim, this paper proposes a new model of international trade in which firms’ interactions are characterized by density externalities. This type of interactions are closely related to Mean Field Game. After showing that this type of interaction includes monopolistic competition, we plead for a dierent equilibrium concept allowing firms with identical characteristics to export to dierent destinations at equilibrium. Thereby we oer a rationale to the findings of Eaton Kortum and Kramarz (2011). Our results are shown to be robust to many dierent specifications of trade costs, consumer preferences and distribution of firms.
Gold nanoisland arrays by repeated deposition and post-deposition annealing for surface-enhanced Raman spectroscopy

Gold nanoisland arrays with well controlled growth were achieved by repeated sputtering deposition and post-deposition annealing processes. When each deposition was set at 5 nm (nominal thickness based on gold mass), the single deposition and annealing process (single process) yielded gold nanoisland arrays with an average diameter of ∼16 nm based on top view scanning electron microscopy (SEM). When the deposition and annealing process was repeated two more times (triple process), top view SEM showed the nanoisland arrays grew to ∼38 nm in average diameter. The surface-enhanced Raman spectroscopy (SERS) measurement indicated that triple processed nanoisland arrays led to the highest SERS enhancement, suggesting the necessity of pursuing nanoislands with larger sizes. The gold nanoisland arrays after the triple process were further sputtered with a final layer of gold thin film at different nominal thicknesses. An optimal nominal thickness for SERS was determined experimentally at ∼40 nm, as a result of the competition between the positive and negative effects of the final gold deposition. Last, the uniformity of the optimized SERS substrate was investigated on a 5 cm × 5 cm platform. SERS measurements demonstrated a relative standard deviation of ∼7% in terms of spectral variation over the entire substrate, rendering the process in the present study a promising fabrication approach for large-scale production of SERS substrates.
How is firing activity of substantia nigra cells regulated? Relevance of pattern‐code in the basal ganglia

The current model of the basal ganglia (BG) assumes that neurons use a firing rate renewal code for movement computing under normal and pathological conditions. Here, we report nonrenewal firing (neuronal firing is influenced by its own previous activity) in cells of the anesthetized rat's substantia nigra (SN). Both compensatory (short interspike intervals (ISIs) are followed by long ISIs and vice versa) and persistent (short and long ISIs cluster for long time periods) nonrenewal activity was found in 52.6% and 33.8% of SN cells, respectively. A compensatory pattern was found in 77.7% of DA cells, but in only 9.8% of GABA‐cells. Conversely, a persistent pattern was observed in 74.6% of GABAergic cells and in only 9.9% of DA cells. These findings indicate two types of nonrenewal firing pattern codes specifically present in SN dopaminergic and GABAergic neurons. Disruption of these patterns may play a role in the pathophysiology of basal ganglia disorders such as Parkinson's disease and dyskinesias. Synapse 49:216–225, 2003. © 2003 Wiley‐Liss, Inc.
A Worldwide Survey of the Current Daily Practice in Liver Surgery

Background: Liver resection remains the mainstay of curative treatment for liver malignancies. A variety of preoperative assessments and surgical techniques have improved the short- and long-term outcomes of liver resection in patients with liver tumors. Recently, laparoscopic hepatectomies have been increasingly performed. The aim of the present study is to survey the current practice of liver surgery in high-volume centers in the world. Methods: A questionnaire on the preoperative assessment for liver surgery, open hepatectomy, and laparoscopic hepatectomy was sent to 94 liver centers in the world. Results: Forty-two centers (45%) responded to this survey (29 Asian, 9 European, and 4 North American centers). All but one of the centers evaluated the future liver remnant (FLR) volume, and 95% of them performed preoperative portal vein embolization to increase the FLR volume. In half of the centers, the required FLR volume was over 30% in patients with normal liver and 50% in patients with cirrhotic liver. To reduce the intraoperative blood loss, half of the centers routinely used Pringle’s maneuver, and 85% restricted the intraoperative fluid infusion to reduce the central venous pressure. More than 10 laparoscopic hepatectomies were performed per year in 62% of the centers, and more than 30 were performed in 26%, respectively. Laparoscopic major hepatectomies were performed in 24%. Two-thirds answered that the laparoscopic approach would be feasible in donor hepatectomy. Conclusion: The evaluation of FLR volume in patients with normal or cirrhotic liver and the usage of preoperative portal vein embolization have become essential practice in more than 90% of the centers. Reduced blood loss has been achieved using Pringle’s maneuver, restriction of fluid infusion, and a variety of surgical devises. The laparoscopic approach is increasingly extended to major hepatectomy or donor hepatectomy.
Aging and sexual health: getting to the problem

Abstract Erectile dysfunction (ED) is one of the most common disorders in male and is often associated with other age-related comorbidities. The aging process affects the structural organization and function of penile erectile components such as smooth muscle cell and vascular architecture. These modifications affect penile hemodynamics by impairing cavernosal smooth muscle cell relaxation, reducing penile elasticity, compliance and promoting fibrosis. This review aims to identify the mechanisms of ED in the penile aging process in experimental and clinical data. It also highlights areas that are in need of more research. The search strategies yielded total records screened from PubMed. Clarification of the molecular mechanisms that accompanies corpus cavernosum aging and aging-associated ED will aid new perspectives in the development of novel mechanism-based therapeutic approaches. Age is not a limiting factor for ED medical management, and it is never too late to treat. Hypogonadism should be managed regardless of age, and synergistic effects have been found during testosterone (T) replacement therapy when used along with oral phosphodiesterase-5 (PDE-5) inhibitors. Therefore, the clinical management of ED related to aging can be done by therapeutic interventions that include PDE-5 inhibitors, and other pharmacological treatments.
Adaptation to College for Students with and without Disabilities: Group Differences and Predictors.

This study investigated differences between attributional style and student adaptation to college for students with and without disabilities. In terms of attributional style, the students with disabilities demonstrated a more internal, stable, and global attributional style for both positive events and negative events. In terms of student adaptation to college, the group of students without disabilities scored higher for overall student adaptation to college, social adjustment, institutional attachment, and semester GPA. Additionally, we explored the ability of six variables to predict student adaptation to college for students with disabilities. Two variables contributed significantly to the prediction: self-advocacy skill and visibility of disability.
Sequences flanking the cAMP responsive core of the HTLV-I tax response elements influence CREB protease sensitivity.

The human T cell leukemia virus type I (HTLV-I) Tax protein activates transcription from the viral long terminal repeat and select cellular promoters by interacting with cellular DNA-binding proteins. The HTLV-I promoter contains three copies of a Tax-responsive element (TRE-1), each of which possesses a core cAMP response element (CRE). The cAMP response element-binding protein, CREB, binds TRE-1 and mediates Tax association with, and transactivation of, the viral promoter. These activities depend on DNA sequences that flank the core CRE. Although CREs are found in a variety of cellular promoters, cellular CREs vary in sequence from TRE-1, especially in the flanking regions, and are generally not Tax responsive. The molecular basis for differential Tax responsiveness of viral and cellular CREs has not been determined. Here we demonstrate that the conformation of CREB is influenced by the nucleotide sequence of its DNA-binding element. CREB showed altered sensitivity to V8, chymotrypsin, and trypsin proteases when bound to the HTLV-I TRE-1 element as compared to the rat somatostatin CRE element. The phosphorylation state of CREB did not influence its protease sensitivity on either element. Sequences flanking the core CRE-binding site in each element were found to specify protease sensitivity. Since the TRE-1-flanking sequences also modulate Tax association with CREB, and Tax transactivation of CREB-dependent LTR transcription, these results suggest that CREB conformation may determine the ability of Tax to bind CREB.
Glass Ceiling and women employees in Asian organizations: a tri-decadal review

The purpose of the paper is to review and analyse different glass ceiling studies conducted in different Asian countries during the three decades after the introduction of the metaphor. It also describes the antecedents and the consequences of the glass ceiling. ,The method chosen for the study was a computerised search of available materials using the keywords relating to glass ceiling in Asia and latest reports from international organisations. ,The perception of glass ceiling existence in Asian countries has been sorted out region-wise. Different factors for glass ceiling have been categorised under different theories. ,The study includes a multiregional aspect of glass ceiling, which will be useful for further studies in this area. The limitation of the study is that it did not assess the awareness and influence of glass ceiling in each industry. ,Since the study showed glass ceiling practices in different countries in Asia, it might help policy makers for making proper decisions for breaking of glass ceiling. ,The study may be a part of empowering women as it analyses areas of inequality and finds out antecedents. ,This paper is the first to shed light on glass ceiling on a multicultural and multiregional aspect.
Indirect binding of human T-cell leukemia virus type I tax1 to a responsive element in the viral long terminal repeat

Several laboratories have demonstrated that tandem copies of the human T-cell leukemia virus type I 21-base-pair (bp) repeat cloned upstream of either a homologous or heterologous promoter increase transcription in the presence of tax1 protein. In this report, we provide evidence for a second tax1-responsive sequence in the viral long terminal repeat. Analysis of human T-cell leukemia virus type I promoter deletion mutants and plasmids containing cloned oligonucleotide motifs demonstrated that this 47-bp sequence, located between -117 and -163, confers responsiveness to tax1. We further demonstrated that proteins present in HeLa nuclear extracts bind specifically to this tax1-responsive sequence. Mutants that affected in vivo activity also decreased in vitro binding. Using an in vitro binding assay, we demonstrated that tax1 interacts indirectly with the 47-bp sequence, most likely through protein-protein interaction. Thus, while tax1 does not bind directly to DNA to enhance transcription, it may influence sequence-specific responses by interacting with the primary DNA-protein complex.
An education program to reduce unnecessary laboratory tests by residents

What are often called “little-ticket” items–X-rays and laboratory tests–account for 25–30% of all health care costs. Two such items were the focus of this study, which took place at an inner-city community health center operated by the Department of Family Medicine of Cook County Hospital and involved 20 family practice residents over a period of nine weeks. The first item was the complete blood count (CBC) with differential, a prototype of a low-cost, high-volume test often ordered by reflex; the second, the thyroid stimulating hormone (TSH) test, a high-cost, low-volume test normally associated with a differential diagnosis or clinical reasoning. Through the use of a simple educational intervention based on quality of care, not cost-containment, and an audit feedback system, the authors were able to reduce significantly the rates of ordering TSH tests (p less than .0001) and CBCs (p = .05). This effect on the rates persisted five months after the intervention terminated. In addition, the percentage of TSH tests clinically indicated by explicit criteria increased significantly (p less than .001) during the intervention. However, this effect showed signs of diminishing five months after the intervention ended. The percentage of CBCs clinically indicated did not change significantly as a result of this intervention.
Processing natural language based query and context sensitive spelling suggestion in information retrieval

This paper present several key issues about modelling and processing natural language based query in information retrieval. On the basis of the sentence-pattern based module, we propose some methodologies. Focusing on misspelling and processing on natural language query, this paper also presents the strategy on context sensitive spelling suggestion as users usually present spelling errors either by accident or the proposed term has ambiguous spelling. Based on the similar comparison between the right terms and the proposed one, the algorithm can not only tolerate misspelling, but present relevant advice. It is useful in the case when user may not know how a proper term is spelled. Furthermore, if more than two correctly spelled terms are nearly tied, it can also select more common or frequently one. According to the users' natural language query, the proposed algorithm can present relevant results or return several suggested alternative queries with the correct spelling.
Jakość rządzenia na poziomie lokalnym a efektywność wykorzystania endogenicznych potencjałów wsi

Rural areas in Poland have endogenous potentials which should become the drivers of sustainable local development. At the same time – as indicated by both the evolution of economic theories related to regional development, as well as researches in the field of institutional economics – the main factors determining growth and economic development are the institutional environment where economic processes are being developed and the quality of institutions per se in se. Among the latter, the quality of governance is of particular importance. It directly affects both the broadly understood institutional environment, as well as it determines the implementation of development policies. In reference to the rural areas and to the use of their endogenous resources the implementation of the rules of good governance by local authorities seems to be very important. In order to measure the quality of governance at the local level and to check how it affects the use of endogenous potentials of rural areas it was proposed to adapt the theory of good governance to the specifics of the functioning of local authorities in Poland. Also special research tools have been developed and empirical research in four locations has been carried out.
A composite sensitivity factor based method for networked distributed generation planning

Distributed generation (DG) can provide multiple benefits to distribution networks such as power loss reduction and voltage stability enhancement. Today's distribution networks are designed with an increased penetration level of DG. In this paper, a novel composite sensitivity factor based method (CSFBM) is proposed for optimizing locations and sizes of network owned DG units to decrease the losses and to improve the voltage stability simultaneously in a distribution network. CSFBM prioritizes the buses which are more sensitive to the losses and the voltage stability and then applies sensitivity factors to settle DG units iteratively. Besides, uncertainties of renewable resource DG outputs are fully considered with a discrete Monte Carlo simulation. CSFBM is tested on two radial distribution systems with different scenarios including single stage and multi-stage planning. In comparison to a multi-objective genetic algorithm, the DG allocations performed by CSFBM are unique satisfying optimization solutions with a much higher efficiency.
RFID tags on cork stoppers for bottle identification

This paper presents the design of two UHF RFID tags in cork substrate. The RFID tags are designed to be compact and conformal to fit within the size and shape of the bottle and barrel stoppers. In a first step, the selected cork material is characterized taking into account the anisotropic properties of cork substrates and after the characterization two RFID tags are designed and optimized to cover a certain read range when placed inside bottle and barrel corks.
In Silico Quantitative Trait Locus Map for Atherosclerosis Susceptibility in Apolipoprotein E–Deficient Mice

Objective—Atherosclerosis susceptibility is a genetic trait that varies between mouse strains. The goal of this study was to use a public mouse single nucleotide polymorphism (SNP) database to define the genetic loci that are associated with this trait, without the need to perform strain intercrosses that are normally required to obtain these loci. Methods and Results—Apolipoprotein E (apoE)–deficient mice on 6 inbred genetic backgrounds were compared for atherosclerosis lesion size in the aortic root in 2 independent studies. After normalization to the C57BL/6 strain that was used in both studies, lesion areas were found in the following rank order: DBA/2J>C57BL/6>129/SV-ter>AKR/J≈BALB/cByJ≈C3H/HeJ. The log lesion difference in phenotypes between each of the 15 heterologous strain pairs was determined. A mouse SNP database was then used to calculate the genetic differences between the 15 strain pairs in partially overlapping 30-cM bins across the mouse genome. Correlation analyses were preformed to analyze the genetic and phenotypic differences among the strain pairs for each genetic region. The genetic regions with the highest correlations define the in silico quantitative trait loci (QTL) associated with the atherosclerosis phenotype. Five in silico atherosclerosis QTL were identified on chromosomes 1, 10, 14, 15, and 18. The loci on chromosomes 1, 10, 14, and 18 overlap with suggestive atherosclerosis QTL identified through analyses of an F2 cohort derived from apoE-deficient mice on the C57BL/6 and FVB/N strains. Conclusions—The 5 identified in silico QTL are candidates for further study to confirm the presence and identity of atherosclerosis susceptibility genes within these loci.
Molecular heterogeneity of B‐lineage diffuse large cell lymphoma

B‐lineage diffuse large cell lymphoma (B‐DLCL) arising de novo is characterized by a marked degree of clinical heterogeneity. To determine whether or not the clinical heterogeneity of de novo B‐DLCL is reflected by heterogeneity in the molecular features of these tumors, we investigated the pattern of distribution of several genetic lesions in 70 cases of de novo B‐DLCL at diagnosis. The panel of genetic lesions tested comprised the molecular alterations most frequently detected in B‐DLCL, including rearrangements of BCL2, BCL6, and MYC as well as deletions of 6q and mutations of TP53. One or more genetic lesions were detected in 39/70 cases of B‐DLCL. Isolated structural alterations of BCL2, BCL6, 6q or TP53 were detected in 8/70, 10/70, 11/70, and 3/70 cases, respectively. No isolated MYC lesions were detected. Six cases carried different combinations of two genetic lesions, including lesions of BCL2 + BCL6 (1 case), BCL2 + MYC (1 case), BCL2 + 6q (2 cases), or BCL6 + 6q (2 cases). One case had accumulated three genetic lesions, namely a rearrangement of BCL2 and BCL6 and a mutation of TP53. Overall, these data show that multiple distinct patterns of genetic lesions may associate with de novo B‐DLCL, indicating that the molecular pathogenesis of this group of lymphomas is characterized by a high degree of molecular heterogeneity. Genes Chromosom Cancer 16:21–30 (1996). © 1996 Wiley‐Liss, Inc.