Miracle-dz/UniFAR-FTUs huggingface dataset:
The carboxyl‐terminal extension on fungal mitochondrial DNA polymerases: identification of a critical region of the enzyme from Saccharomyces cerevisiae

Fungal mitochondrial DNA (mtDNA) polymerases, in comparison to their metazoan counterparts, harbour unique carboxyl‐terminal extensions (CTEs) of varying lengths and unknown function. To determine the essential regions of the 279 residue CTE of the yeast enzyme (Mip1p), several CTE‐truncation variants were expressed in Saccharomyces cerevisiae. The respiratory competence of mip1Δ175 cells, in which Mip1p lacks the C‐terminal 175 residues, is indistinguishable from that of wild‐type. In contrast, strains harbouring Mip1pΔ351 and Mip1pΔ279 rapidly lose mtDNA. Approximately one in six mip1Δ216 transformants grew on glycerol, albeit poorly. Fluorescence microscopy and Southern blot analysis revealed lower levels of mtDNA in these cells, and the rapid loss of mtDNA during fermentative, but not respiratory, growth. Therefore, only the polymerase‐proximal segment of the Mip1p CTE is necessary for mitochondrial function. Comparison of this essential segment with the sequences of other fungal mtDNA polymerases revealed novel features shared among the mtDNA polymerases of the Saccharomycetales. Copyright © 2006 John Wiley & Sons, Ltd.
The increasing problem of unusual pancreatic tumors.

HYPOTHESIS Patients presenting with a pancreatic mass often have a curable lesion rather than the more common adenocarcinoma. Greater awareness of this among nonsurgeons is necessary. DESIGN Retrospective case series. SETTING Tertiary care referral hospital. PATIENTS All patients who presented with a pancreatic mass during the 8 years from 1990 to 1998 were studied. Patients with a history of chronic pancreatitis, a functioning pancreatic neuroendocrine tumor, or pancreatic adenocarcinoma were excluded. Forty patients were identified, demographic and clinical characteristics recorded, and long-term follow-up obtained. INTERVENTIONS Therapy included either a Whipple procedure or distal pancreatectomy. Two patients underwent a biliary bypass. MAIN OUTCOME MEASURES Tumor histology, morbidity, and survival. RESULTS Three hundred thirty-six patients with a pancreatic mass were treated during this 8-year period. Two hundred ninety-six of these had pancreatic adenocarcinoma. Forty (11.9%) of the 336 patients had other types of pancreatic tumors. Two thirds of these patients were female, with an average age of 57 years. Seventy-five percent of these tumors were either malignant or potentially malignant. In several instances, cystic tumors were diagnosed as inflammatory pseudocysts and managed accordingly. Fourteen (35%) of 40 patients had no symptoms and their tumor was found on a computed tomographic scan performed for another indication. Percutaneous biopsy was performed in 9 patients, of whom 5 were assigned an incorrect diagnosis. There were no operative deaths, although the postoperative complication rate was 23%. CONCLUSIONS In this series, nearly 12% of patients presenting with a pancreatic mass did not have pancreatic adenocarcinoma, but rather more favorable lesions amenable to operation. Preoperative biopsy should not be carried out. Curative procedures can be safely performed in centers seeing a large number of patients with pancreatic tumors, and the long-term results of extirpation are excellent.
Spanning forests in regular planar maps (conference version)

We address the enumeration of $p$-valent planar maps equipped with a spanning forest, with a weight $z$ per face and a weight $u$ per component of the forest. Equivalently, we count regular maps equipped with a spanning tree, with a weight $z$ per face and a weight $\mu:=u+1$ per internally active edge, in the sense of Tutte. This enumeration problem corresponds to the limit $q \rightarrow 0$ of the $q$-state Potts model on the (dual) $p$-angulations. Our approach is purely combinatorial. The generating function, denoted by $F(z,u)$, is expressed in terms of a pair of series defined by an implicit system involving doubly hypergeometric functions. We derive from this system that $F(z,u)$ is $\textit{differentially algebraic}$, that is, satisfies a differential equation (in $z$) with polynomial coefficients in $z$ and $u$. This has recently been proved for the more general Potts model on 3-valent maps, but via a much more involved and less combinatorial proof. For $u \geq -1$, we study the singularities of $F(z,u)$ and the corresponding asymptotic behaviour of its $n^{\mathrm{th}}$ coefficient. For $u > 0$, we find the standard asymptotic behaviour of planar maps, with a subexponential factor $n^{-5/2}$. At $u=0$ we witness a phase transition with a factor $n^{-3}$. When $u \in[-1,0)$, we obtain an extremely unusual behaviour in $n^{-3}/(\log n)^2$. To our knowledge, this is a new ''universality class'' of planar maps.
SENTIMENT ANALYSIS WITH RECURRENT NEURAL NETWORK AND UNSUPERVISED NEURAL LANGUAGE MODEL Ph

This paper describes a simple and efficient Neural Language Model approach for text classification that relies only on unsupervised word representation inputs. Our model employs Recurrent Neural Network Long Short-Term Memory (RNN-LSTM), on top of pre-trained word vectors for sentence-level classification tasks. In our hypothesis we argue that using word vectors obtained from an unsupervised neural language model as an extra feature with RNN-LSTM for Natural Language Processing (NLP) system can increase the performance of the system. Our technique has improved the model to capture syntactic and semantic word relationships. We show that simple RNN-LSTM with word2vec achieves excellent result on IMDB Stanford benchmark for sentiment analysis task.
Virtual mechanism approach for dual-arm manipulation

SUMMARY We propose a novel control approach for cooperative dual-arm manipulation tasks. Our scheme has three typical features: (1) the task performed by two robots is represented as a motion of a virtual mechanism and the task execution is accomplished by controlling the virtual mechanism; (2) the two arms and the task form a joined kinematic chain; (3) the scheme allows a cooperative dual-arm system to perform the task also when robot base is moving. The calculation of the Jacobian matrix of a chained two-arm mechanisms is based on a methodology which is using the Jacobian matrices of particular robot mechanisms and their end-effector positions and orientations. The proposed algorithm for dual-arm manipulation is verified by simulations of two cooperating planar robots and by experiments on a dual-arm robot consisting of two KUKA LWR arms.
The Multiple Carrier Model of Nonribosomal Peptide Biosynthesis at Modular Multienzymatic Templates*

Gramicidin S synthetase 1 and 2 were affinity-labeled at their thiolation centers either by thioesterification with the amino acid substrate or by specific alkylation with the thiol reagent N-ethylmaleimide in combination with a substrate protection technique. The labeled proteins were digested either chemically by cyanogen bromide or by proteases. An efficient multistep high pressure liquid chromatography methodology was developed and used to isolate the active site peptide fragments of all five thiolation centers of gramicidin S synthetase in pure form. The structures of these fragments are investigated by N-terminal sequencing, mass spectrometry, and amino acid analysis. Each of the active site peptide fragments contains the consensus motif LGG(H/D)S(L/I), which is specific for thioester formation in nonribosomal peptide biosynthesis. It was demonstrated that a 4′-phosphopantetheine cofactor is attached to the central serine of the thiolation motif in each amino acid-activating module of the gramicidin S synthetase multienzyme system forming the thioester binding sites for the amino acid substrates and catalyzing the elongation process. Our data are strong support for a “multiple carrier model” of nonribosomal peptide biosynthesis at multifunctional templates, which is discussed in detail.
Extracting Jacobi Structures in Reeb Spaces

Jacobi sets have been identified as significant in multi-field topological analysis, but are defined in the domain of the data rather than in the Reeb Space. This distinction is significant, as exploiting multi-field topology actually depends on the projection of the Jacobi set into the Reeb Space, and the details of its internal structure. We therefore introduce the Jacobi Structure of a Reeb Space which describes this, explain its relationships with both the Jacobi Set and Fiber Analysis in mathematical topology, give an algorithm for computing the Jacobi Structure recursively using a Multi-Dimensional Reeb Graph and illustrate it using an early implementation in VTK.
In vivo tumor cell rejection induced by NK cell inhibitory receptor blockade: Maintained tolerance to normal cells even in the presence of IL‐2

Missing‐self‐reactivity can be mimicked by blocking self‐specific inhibitory receptors on NK cells, leading to increased rejection of syngeneic tumor cells. Using a mouse model, we investigated whether Ab‐mediated blocking of inhibitory receptors, to a degree where NK cells rejected syngeneic tumor cells, would still allow self‐tolerance toward normal syngeneic cells. Ly49C/I inhibitory receptors on C57BL/6 (H‐2b) NK cells were blocked with F(ab')2 fragments of the mAb 5E6. Inhibitory receptor blockade in vivo caused rejection of i.v. inoculated fluorescence‐labeled syngeneic lymphoma line cells but not of syngeneic spleen cells, BM cells or lymphoblasts. The selective rejection of tumor cells was NK cell‐dependent and specifically induced by Ly49C/I blockade. Moreover, selective tumor rejection was maintained after treatment with 5E6 F(ab')2 for 9 wk, arguing against the induction of NK cell anergy or autoreactivity during this time. Combination therapy using 5E6 F(ab')2 together with high dose IL‐2 treatment further increased lymphoma cell rejection. In addition, combination therapy reduced growth of melanoma cell line tumors established by s.c. inoculation 3 days before start of treatment. Our results demonstrate that inhibitory receptor blockade does not result in attack on normal cells, despite potent reactivity against MHC class I‐expressing tumors.
An Overlapping Community Detection Algorithm Based on Link Clustering in Complex Networks

Community detection has important significance for understanding network topology and analyzing network function. It has been shown that there are high overlapping community structures in the complex networks. However, it is difficult to detect these structures for the existing community detection algorithms. This paper proposes an algorithm (CLCD) to detect high overlapping community structures. This algorithm starts from the perspective of the link. Through selecting a core link, this algorithm attracts links in the outer space to join in the community which contains the core link only in the beginning. Finally, transform link communities to node communities. The global optimal overlapping community structures will be formed after adjusting the node communities. This algorithm can get the number of communities automatically without inputting additional parameters. The examples of application to both artificial networks and real networks give better results on detecting high overlapping community structures.
Environmental influence on L1 retrotransposons in the adult hippocampus

It is well established that neuronal circuits can be shaped by experience. Neuronal plasticity can be achieved by synaptic competitive interactions and the addition of new neuronal units in neurogenic regions of the adult brain. Recent data have suggested that neuronal progenitor cells can accommodate somatic LINE‐1 (Long Interspersed Nuclear Elements‐1 or L1) retrotransposition. Genomic L1 insertions may up‐ or down‐regulate transcriptional control of gene expression. Here, we show that exercise has a positive effect on a L1‐EGFP reporter in vivo. We found that neurons from mice that experience voluntary exercise are more likely to activate an EGFP reporter marker, representing L1 insertions in the brain, when compared with sedentary animals. In the hippocampus, a neurogenic region of the adult brain, EGFP expression is mainly found in cells localized in the subgranular layer of the dentate gyrus. This observation implies that neuronal progenitor cells may support de novo retrotransposition upon exposure to a new environment. Such evidence suggests that experience‐dependent L1 retrotransposition may contribute to the physiological consequences of neuronal plasticity. © 2009 Wiley‐Liss, Inc.
Chapter 28 Multiple Antigen Immunostaining Procedures

Detection of multiple antigens in the same tissue section can be done by combining a range of immunohisto/cytochemical techniques based either on light microscopic chromogenic precipitates or fluorochrome labeling. Light microscopic techniques preferred for this purpose use combinations of immunogold silver staining (black precipitate), immunoperoxidase, immunoalkaline phosphatase and immunogalactosidase methods using chromogens of different colors. Fluorochrome labels favored for these combinations include AMCA (blue), FITC (green), rhodamine (orange-red) and Cy5 (far red), their matching synthetic members from the Alexa series, or quantum dots. Antibodies directly labeled or those from noncross-reacting animal species (e.g., mouse, rabbit, goat, guinea pig etc.) can be applied simultaneously. When the antigens of interest are in separate cells or cell compartments (e.g., in cell membrane, cytoplasm or nucleus), and only cross-reacting antibodies are available, there have also been ways of avoiding unwanted cross-talk. These include the exploitation of the shielding effect of chromogens; inactivation of immuno-sequences of the first staining by using either acidic elution, formaldehyde fixation or microwave heating; combining unlabeled and hapten-labeled antibodies; or using labeled monovalent F(ab) secondary antibodies. In this chapter we briefly discuss the principle of multiple antigen immunolabeling and provide useful protocols for its performance.
Locating cities on global circuits

This paper discusses the cities that have the resources which enable firms and markets to be global. It considers the new intensity and complexity of globally-connected systems of production, finance and management which may disperse production, yet need (relatively few) networks of cities to provide their organizational and management architecture. This produces new geographies and hierarchies of centrality - particular cities and regions that have key roles in globalization. Many such cities become far more closely linked to the global economy than to their regional or national economies - and this can have harsh consequences locally, pushing out firms and people that are not within the internationalized sector. The paper discusses why certain cities retain such importance, when production is so dispersed and when telecommunications and rapid transport systems have limited the advantages of spatial concentration. It also considers the dependence of global cities on each other; a crisis in one key centre often brings problems rather than opportunities for others.
A new tunneling path for reactions such as H+H2→H2+H

The standard tunneling path in transition state theory for reactions such as H+H2→H2+H has been the so‐called reaction path, namely the path of steepest ascent to the saddle point. This path is now known to give numerical results for the reaction probability which are in disagreement with the exact quantum mechanical ones by an order of magnitude at low tunneling energies. A new tunneling path corresponding to a line of vibrational endpoints is proposed. It is much shorter and is shown to give results in agreement with the quantum ones to within about a factor of two. A semiclassical basis for choosing this new path is given.
The effect of molybdenum-induced copper deficiency on acute-phase protein concentrations, superoxide dismutase activity, leukocyte numbers, and lymphocyte proliferation in beef heifers inoculated with bovine herpesvirus-1.

This study was conducted to determine the effect of Cu deficiency on acute-phase protein concentrations, superoxide dismutase activity, leukocyte numbers, and lymphocyte proliferation in heifers inoculated with live bovine herpesvirus-1 (BHV-1). Hereford x Angus heifers were allotted by weight and initial liver Cu concentrations into molybdenum (Mo)-supplemented (n = 6) or control (n = 6) groups. Control heifers were fed a basal diet supplemented with Cu-sulfate to achieve a dietary concentration of 8 ppm of Cu. The Mo-supplemented heifers received the basal diet supplemented with Mo to achieve a dietary Mo:Cu ratio of 2.5:1 and with sulfur at . 3% of the diet. All treatments were delivered for 129 d, when heifers were inoculated intranasally with BHV-1. To ensure adequate Cu stores before viral challenge, control heifers were given a cupric glycinate injection on d 100 of treatment. On d 129, Mo-supplemented heifers were considered Cu-deficient (liver Cu = 23.2 and 90.1 ppm for Mo-supplemented and control, respectively). Neutrophils were increased (P < .01) on d 129 in Mo-supplemented heifers. Ceruloplasmin, a copper-dependent acute-phase protein, increased (P < .01) by 48 h after challenge in control but not in Mo-supplemented heifers. Fibrinogen, an acute-phase protein not containing copper, increased by 48 h after challenge in Mo-supplemented but not in control heifers. Erythrocyte superoxide dismutase (SOD) activity was less (P < .05) in Mo-supplemented heifers on d 129. Viral challenge had no effect on SOD activity. Lymphocyte proliferative response to phytohemagglutinin stimulation was greater (P < .01) for Mo-supplemented heifers following BHV-1 challenge. No differences were detected when lymphocytes were stimulated with concanavalin-A or pokeweed mitogens. These data indicate that Cu deficiency alters the acute-phase protein response to viral infection and may affect lymphocyte responsiveness to mitogen stimulation.
Repbase Update, a database of eukaryotic repetitive elements

Repbase Update is a comprehensive database of repetitive elements from diverse eukaryotic organisms. Currently, it contains over 3600 annotated sequences representing different families and subfamilies of repeats, many of which are unreported anywhere else. Each sequence is accompanied by a short description and references to the original contributors. Repbase Update includes Repbase Reports, an electronic journal publishing newly discovered transposable elements, and the Transposon Pub, a web-based browser of selected chromosomal maps of transposable elements. Sequences from Repbase Update are used to screen and annotate repetitive elements using programs such as Censor and RepeatMasker. Repbase Update is available on the worldwide web at http://www.girinst. org/Repbase_Update. html.
Both CD4 and CD8 T Cells Mediate Equally Effective In Vivo Tumor Treatment When Engineered with a Highly Avid TCR Targeting Tyrosinase

Tyrosinase, an enzyme involved in melanin synthesis, is expressed in nearly all primary and metastatic melanoma lesions and thus is an attractive target for TCR-based gene therapy using adoptive cell transfer. The TCR α- and β-chain genes from a tumor-infiltrating lymphocyte, which recognized the tyrosinase 368–376 peptide in the context of HLA-A2, were cloned into a γ-retroviral vector. Following transduction of PBL, specific reactivity was confirmed by cytokine production following coculture with tumor targets. Experiments using Ab blockade and CD4/CD8 sorting of the transduced PBLs demonstrated that this antityrosinase TCR was CD4/CD8 independent. The introduction of a second disulfide bond between the TCR constant regions and/or creation of a chimeric protein in which the human constant regions were replaced by murine homologs resulted in enhanced TCR expression as demonstrated by tetramer staining and improved tumor reactivity that was comparable to PBL transduced with either anti-melanoma Ag recognized by T cells-1 or anti-gp100 TCR vectors currently used in clinical trials. The chimeric TCR also allowed us to test antitumor function of in HLA-A2/Kb–transgenic mice. Transfer of the antityrosinase TCR into mouse splenocytes conferred CD4/CD8-independent, HLA-A2–restricted Ag reactivity against B16/A2Kb murine melanoma in vitro. Furthermore, adoptive transfer of transduced splenocytes mediated B16/A2Kb melanoma tumor regression in lymphodepleted mice, and, surprisingly, both CD8 and CD4 T cells were equally effective in mediating tumor regression. These results suggest that this highly active tyrosinase-specific TCR could be of value in adoptive cell transfer for melanoma.
Team cooperation incorporating inequity aversion and social norms

It is difficult to achieve cooperation in team production because there is an intrinsic free-riding problem. This paper incorporates inequity aversion, which has been ignored by the standard contract theory, but has also been proven by a series of game experiments, to systematically investigate how peer pressures stem from horizontal monitor and comparison, why peer sanction with cost still will be carried out definitely, how peer pressures facilitate team cooperation, and how social norms further ensure cooperation as a unique equilibrium. It is found that the internal peer pressure can realize team cooperation only under very strong inequity aversion, while the external peer pressure can achieve team cooperation under comparatively weak inequity aversion, and only in social norms by which many enough peers are expected to collaborate initiatively, can team cooperation be implemented uniquely. Therefore, to cultivate inequity aversion of staffs and to develop social norm with cooperative expectation surely can facilitate teamwork.
E3 Ubiquitin Ligase RNF31 Cooperates with DAX-1 in Transcriptional Repression of Steroidogenesis

ABSTRACT Genetic and experimental evidence points to a critical involvement of the atypical mammalian orphan receptor DAX-1 in reproductive development and steroidogenesis. Unlike conventional nuclear receptors, DAX-1 appears not to function as a DNA-bound transcription factor. Instead, it has acquired the capability to act as a transcriptional corepressor of steroidogenic factor 1 (SF-1). The interplay of DAX-1 and SF-1 is considered a central, presumably ligand-independent element of adrenogonadal development and function that requires tight regulation. This raises a substantial interest in identifying its modulators and the regulatory signals involved. Here, we uncover molecular mechanisms that link DAX-1 to the ubiquitin modification system via functional interaction with the E3 ubiquitin ligase RNF31. We demonstrate that RNF31 is coexpressed with DAX-1 in steroidogenic tissues and participates in repressing steroidogenic gene expression. We provide evidence for the in vivo existence of a corepressor complex containing RNF31 and DAX-1 at the promoters of the StAR and CYP19 genes. Our data suggest that RNF31 functions to stabilize DAX-1, which might be linked to DAX-1 monoubiquitination. In conclusion, RNF31 appears to be required for DAX-1 to repress transcription, provides means to regulate DAX-1 in ligand-independent ways, and emerges as a relevant coregulator of steroidogenic pathways governing physiology and disease.