Miracle-dz/UniFAR-FTUs huggingface dataset:
A model selection criterion for model-based clustering of annotated gene expression data

Abstract In co-expression analyses of gene expression data, it is often of interest to interpret clusters of co-expressed genes with respect to a set of external information, such as a potentially incomplete list of functional properties for which a subset of genes may be annotated. Based on the framework of finite mixture models, we propose a model selection criterion that takes into account such external gene annotations, providing an efficient tool for selecting a relevant number of clusters and clustering model. This criterion, called the integrated completed annotated likelihood (ICAL), is defined by adding an entropy term to a penalized likelihood to measure the concordance between a clustering partition and the external annotation information. The ICAL leads to the choice of a model that is more easily interpretable with respect to the known functional gene annotations. We illustrate the interest of this model selection criterion in conjunction with Gaussian mixture models on simulated gene expression data and on real RNA-seq data.
Role of Glutamine Synthetase in Nitrogen Metabolite Repression in Aspergillus nidulans

ABSTRACT Glutamine synthetase (GS), EC 6.3. 1.2 , is a central enzyme in the assimilation of nitrogen and the biosynthesis of glutamine. We have isolated the Aspergillus nidulans glnA gene encoding GS and have shown that glnA encodes a highly expressed but not highly regulated mRNA. Inactivation of glnA results in an absolute glutamine requirement, indicating that GS is responsible for the synthesis of this essential amino acid. Even when supplemented with high levels of glutamine, strains lacking a functionalglnA gene have an inhibited morphology, and a wide range of compounds have been shown to interfere with repair of the glutamine auxotrophy. Heterologous expression of the prokaryotic Anabaena glnA gene from the A. nidulans alcA promoter allowed full complementation of the A. nidulans glnAΔ mutation. However, the A. nidulans fluG gene, which encodes a protein with similarity to prokaryotic GS, did not replace A. nidulans glnA function when similarly expressed. Our studies with theglnAΔ mutant confirm that glutamine, and not GS, is the key effector of nitrogen metabolite repression. Additionally, ammonium and its immediate product glutamate may also act directly to signal nitrogen sufficiency.
Intravenous vs. intraprostatic administration of N‐methyl‐N‐nitrosourea to induce prostate cancer in rats

To develop an improved model of human prostate cancer, 16‐wk‐old Wistar rats were treated orally for 18 days with the antiandrogen, flutamide (50 mg/kg body weight[BW]/day), weight followed by 3 days of s.c. testosterone (100 mg/kg BW). These were the only treatments the control animals received (Group 1, n = 10). On the day after the third testosterone injection, N‐methyl‐N‐nitorsourea (MNU) was administered via the tail vein at a dose of 50 mg/kg BW (Groups 2, n = 40 and 3, n = 20); in some rats, a second dose was delivered by the same route 22 wk later (Group 3). A smaller dose of MNU (15 mg/kg BW) was administered intraprostatically Group 4, n = 20) to a fourth group. In Groups 2, 3, and 4, silastic capsules containing testosterone were implanted s.c. approximately every 6 wk beginning 1 wk post‐MNU. Accessory sex gland tumors arose in MNU‐treated rats in Group 2 (12/40, 30%), Group 3 (8/20 40%), and Group 4 (8/20, 40%); 90% were macroscopic (25/28). There were no neoplasms in these organs in the control rats (Group 1, 0/10). These accessory sex gland neoplasms were adenocarcinomas or undifferentiated carcinomas which appeared to be derived from the prostate based on location and histological characteristics, although the size and spread of some of the tumors precluded definitive localization of the tissue of origin. The incidence of these neoplasms was similar in rats given a single dose of MNU intraprostatically or two doses of MNU i.v. , but the animals treated intraprostatically maintained higher body weights and developed fewer extraneous tumors. The average (± SD) latent period for clinical or postmortem detection of prostate neoplasia after MNU was shortest in the rats given two i.v. doses (39 ± 3 wk) compared with the single i.v. dose (45 ± 6 wk) or an intraprostatic dose (56 ± 7 wk). In 57% of the cases (16/28), the prostate tumors metastasized to distant sites. An activating point mutation was detected in codon 12 of the Ki‐ras oncogene in the MNU‐induced primary prostate tumors (8/10 examined), and metastases arising from these prostate tumors (2/3) but was absent in normal prostate tissue (0/6). This study demonstrates that two systemic doses of MNU increase the incidence and decrease the latency of prostate neoplasms compared with a single dose, and that a single dose of MNU injected intraprostatically induces prostate adenocarcinoma without many of the other tumors and weight loss typically found after i.v. administration. © 1995 Wiley‐Liss, Inc.
Low serum testosterone and increased diastolic ocular perfusion pressure: a risk for retinal microvasculature.

BACKGROUND Low levels of testosterone in men and changes in retinal microvascular calibre are both associated with hypertension and cardiovascular disease risk. Sex hormones are also associated with blood flow in microvascular beds which might be a key intermediate mechanism in the development of hypertension. Whether a direct association between endogenous testosterone and retinal microvascular calibre exists is currently unknown. We aimed to determine whether testosterone is independently associated with ocular perfusion via a possible association with retinal vascular calibre or whether it plays only a secondary role via its effect on blood pressure in a bi-ethnic male cohort. PROBANDS AND METHODS A total of 72 black and 81 white men (28-68 years of age) from the follow-up phase of the Sympathetic activity and Ambulatory Blood Pressure in Africans (SABPA) study were included in this sub-study. Ambulatory pulse pressure and intraocular perfusion pressures were obtained, while metabolic variables and testosterone were measured from fasting venous blood samples. Retinal vascular calibre was quantified from digital photographs using standardised protocols. RESULTS The black men revealed a poorer cardiometabolic profile and higher pulsatile pressure (>50 mm Hg), intraocular pressure and diastolic ocular perfusion pressure than the white men (p≤0.05). Only in the white men was free testosterone positively associated with retinal calibre, i.e. arterio-venular ratio and central retinal arterial calibre and inversely with central retinal venular calibre. These associations were not found in the black men, independent of whether pulse pressure and ocular perfusion pressure were part of the model. CONCLUSIONS These results suggest an independent, protective effect of testosterone on the retinal vasculature where an apparent vasodilatory response in the retinal resistance microvessels was observed in white men.
The oestrogenic potency of various contraceptive steroids as determined by their effects on transcortin-binding capacity.

Various contraceptive steroids were analyzed for their estrogenic potency in the human using changes in the cortisol-binding capacity of (TC-BC) transcortin as a parameter. A linear dose-related elevation of TC-BC was recorded in response to increasing amounts of (EE) ethinyl estradiol. Mestranol (EEME) given in the same galenical preparation as EE proved to be only 64% as potent. Megestrol acetate dl-norgestrel norethindrone and its acetate failed to influence TC-BC while norethynodrel induced a significant rise. This effect is apparently due to both the inherent estrogenic activity of norethynodrel and its contamination with EEME. The administration of combined (OCs) oral contraceptives resulted in a significant elevation of TC-BC. The drugs studied were (in order to increasing total estrogenicity) 50 mcg EEME + 1 mg norethindrone 35 mcg EE + 0.25 mg d-norgestrel 100 mcg EEME + 2 mg norethindrone 50 mcg EE + 0.25 mg d-norgestrel and 100 mcg EEME + 0.25 mg norethynodrel. The observed rise in transcortin activity appears to depend primarily on the chemical structure and dosage of the estrogen component. These findings clearly indicate that the administration of conventional OCs even those containing low estrogen doses does not cause an estrogen deficiency but rather an estrogen oversupply of the female organism. (Authors modified)
Wyner-Ziv coding of depth maps exploiting color motion information

Distributed Video Coding of multi-view data and depth maps is an interesting and challenging research field, whose interest is growing thanks to the recent advances in depth estimation and the development of affordable devices able to acquire depth information. In applications like video surveillance and object tracking, the availability of depth data can be beneficial and allow for more accurate processing. In these scenarios, the encoding complexity is typically limited and therefore distributed coding approaches are desirable. In this paper a novel algorithm for distributed compression of depth maps exploiting corresponding color information is proposed. Due to the high correlation of the motion in color and corresponding depth videos, motion information from the decoded color signal can effectively be exploited to generate accurate side information for the depth signal, allowing for higher rate-distortion performance without increasing the delay at the decoder side. The proposed scheme has been evaluated against state-of-the-art distributed video coding techniques applied on depth data. Experimental results show that the proposed algorithm can provide PSNR improvement between 2.18 dB and 3.40 dB on depth data compared to the reference DISCOVER decoder, for GOP 2 and QCIF resolution.
Investor Reaction to $Firm or #CEO Use of Twitter for Negative Disclosures

We examine whether CEOs are able to influence how investors react to a negative earnings surprise by directly communicating with them via Twitter prior to the earnings surprise. Results show that investors exhibit higher levels of trust and are more willing to invest in a firm when the firm’s CEO communicates broad firm news followed by a negative earnings surprise through a personal Twitter account than when the news and surprise comes from the CEO via a website or from the firm’s Investor Relations Twitter account or website. Further analysis reveals that direct communications from the CEO through a personal Twitter account help build more trust in the CEO, which leads investors to discount the subsequent negative surprise as a one-time event. We also find that repeated exposure to negative news through the Investor Relation’s Twitter account has a strong negative influence on investors’ investment decisions. Our results have implications for firms and executives who are considering the costs and benefits of directly communicating with investors via Twitter.
Non-mechanical beam scanner integrated VCSEL for solid state LiDAR

We demonstrate the monolithic integration of a non-mechanical beam scanner and VCSEL for solid state LiDAR. A beam deflection is realized by using the electro-thermally tunable VCSEL coupled to a slow light SOA with a large angular dispersion. We obtained the maximum deflection angle of over 13° and a narrow divergence of below 0.15°.
An Explicit Congestion Control Protocol Based on Bandwidth Estimation

Explicit feedback based congestion control schemes can capture network congestion status more accurately than pure end-to-end schemes. However, some of such schemes require modifying IP header in order to achieve near optimal performance, which incurs complicated computation in routers as well as makes them difficult to deploy in real networks. In contrast, the VCP protocol achieves good performance by using the two existing ECN bits in the IP header for feedback, but its convergence speed is relatively low due to insufficient congestion feedback. In this paper, we propose VCP-BE, a protocol based on VCP and uses end-to-end bandwidth estimation to obtain high resolution congestion estimation. With the estimated available bandwidth and ECN feedback, VCP-BE adjusts the congestion window more precisely than VCP thus converges much faster. Simulation results show that VCP-BE outperforms VCP and MLCP, achieving high efficiency and reasonable fairness.
Studies on the synthesis and opioid agonistic activities of mitragynine-related indole alkaloids: discovery of opioid agonists structurally different from other opioid ligands.

Mitragynine (1) is a major alkaloidal component in the Thai traditional medicinal herb, Mitragyna speciosa, and has been proven to exhibit analgesic activity mediated by opioid receptors. By utilizing this natural product as a lead compound, synthesis of some derivatives, evaluations of the structure-activity relationship, and surveys of the intrinsic activities and potencies on opioid receptors were performed with guinea pig ileum. The affinities of some compounds for mu-, delta-, and kappa-receptors were determined in a receptor binding assay. The essential structural moieties in the Corynanthe type indole alkaloids for inducing the opioid agonistic activity were also clarified. The oxidative derivatives of mitragynine, i.e., mitragynine pseudoindoxyl (2) and 7-hydroxymitragynine (12), were found as opioid agonists with higher potency than morphine in the experiment with guinea pig ileum. In addition, 2 induced an analgesic activity in the tail flick test in mice.
Detecting PCB component placement defects by genetic programming

A novel approach is proposed in this study, which is to evolve visual inspection programs for automatic defect detection on populated printed circuit boards. This GP-based method does not require knowledge of the layout design of a board, nor relevant domain knowledge such as lighting conditions and visual characteristics of the components. Furthermore, conventional image operators are not required to perform the detection. The experiments show that these evolved GP programs can identify all the faults while some suspicious areas are also highlighted. By this GP approach, manual inspection effort can be dramatically reduced. In addition, an evolved GP detection program can readily work on different types of boards without re-training.
Site-specific deoxynucleotide substitutions in yeast U 6 snRNA block splicing of pre-mRNA in vitro process of spliceosome

Division of Biology 147-75, California Institute of Technology, ated, and U4 may leave the spliceosome (Pikielny et al., Pasadena, CA 91125, USA 1986; Cheng and Abelson, 1987; Lamond et al., 1988; 1Present address: The Victor Chang Cardiac Research Institute, Yean and Lin, 1991). Dissociation of U4–U6 allows a 5 St Vincent’s Medical Centre, 376 Victoria Street, Darlinghurst, region of the U6 conserved domain to base-pair with U2 NSW 2010, Australia snRNA, thus forming U2–U6 helix I in fully assembled 2Corresponding author spliceosomes (Madhani and Guthrie, 1992) (see model e-mail: abelsonj@starbase1.caltech.edu of the fully assembled yeast spliceosome, Figure 1).
Artificial neural networks based myoelectric control system for automatic assistance in hand rehabilitation

Myoelectric control is using electromyography (EMG) signal as a source of control, with this technique, we can control any computer based system such as robots, devices or even virtual objects. The tendon gliding exercise is one of the most common hand's rehabilitation exercises. In this paper, we present a patterns recognition based myoelectric control system (MCS) for the automatic assistance in tendon gliding exercise. The user is assisted by visual indicators and demo videos. EMG patterns recognition is done with EMG features and a multi-layer Artificial neural network (ANN), the ANN classifier output is used to synchronize the demo video with the detected movement, the transition between states is done automatically when the current state's movement is correct and the required number of repetition is reached. The ANN learning is done using back-propagation algorithm, we have used only two sEMG electrodes and four common used timedomain EMG feature extraction methods, the features quality is evaluated by the average Rand index using eight unsupervised clustering algorithms. The efficacy of the proposed method is experimentally validated with five able-bodied subjects, where we have reached an average classification accuracy of 95.11% and a processing time less than 300ms.
Revisiting the corporate social performance‐financial performance link: A replication of waddock and graves

R esearch summary: In this study, we revisit the relationship between corporate social performance ( CSP) and corporate financial performance ( CFP) by conducting a replication of Waddock and Graves (1997). Using 1990 KLD ratings as the CSP measure, the original study reports a positive bidirectional relationship between CSP and CFP. However, our replication analyses with a larger sample over a longer time period indicate that the findings of the original study may not be generalizable to different samples. We argue that our replication casts doubt on the original study and can serve as a starting point to reconsider the CSP-CFP relationship. Based on the findings of our replication, we discuss the differences between the replication results and the original findings, and then suggest several approaches to revise and extend the original study. M anagerial summary: Advocates of corporate social performance ( CSP) have long argued that 'doing good leads to doing well. ' However, the evidence to support this argument is not strongly convincing, and managers hence doubt whether better CSP leads to improved corporate financial performance ( CFP). In this article, we directly examine the relationship between CSP and CFP. Our article reports that CSP may not have a positive influence on CFP. Instead, our article shows the complexity of the relationship between CSP and CFP. Therefore, we cannot simply argue that doing good will necessarily lead to doing well. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]
The OAuth 2.0 Authorization Framework: Holder-of-the-Key Token Usage

OAuth 2.0 deployments currently rely on bearer tokens for securing access to protected resources. Bearer tokens require Transport Layer Security to be used between an OAuth client and the resource server when presenting the access token. The security model is based on proof-of-possession: access token storage and transfer has to be done with care to prevent leakage. There are, however, use cases that require a more active involvement of the OAuth client for an increased level of security, particularly to secure against token leakage. This document specifies an OAuth security framework using the holder-of- the-key concept, which requires the OAuth client when presenting an OAuth access token to also demonstrate knowledge of keying material that is bound to the token.
The Mitochondrial Cycle of Arabidopsis Shoot Apical Meristem and Leaf Primordium Meristematic Cells Is Defined by a Perinuclear Tentaculate/Cage-Like Mitochondrion1[W][OA]

Plant cells exhibit a high rate of mitochondrial DNA (mtDNA) recombination. This implies that before cytokinesis, the different mitochondrial compartments must fuse to allow for mtDNA intermixing. When and how the conditions for mtDNA intermixing are established are largely unknown. We have investigated the cell cycle-dependent changes in mitochondrial architecture in different Arabidopsis (Arabidopsis thaliana) cell types using confocal microscopy, conventional, and three-dimensional electron microscopy techniques. Whereas mitochondria of cells from most plant organs are always small and dispersed, shoot apical and leaf primordial meristematic cells contain small, discrete mitochondria in the cell periphery and one large, mitochondrial mass in the perinuclear region. Serial thin-section reconstructions of high-pressure-frozen shoot apical meristem cells demonstrate that during G1 through S phase, the large, central mitochondrion has a tentaculate morphology and wraps around one nuclear pole. In G2, both types of mitochondria double their volume, and the large mitochondrion extends around the nucleus to establish a second sheet-like domain at the opposite nuclear pole. During mitosis, approximately 60% of the smaller mitochondria fuse with the large mitochondrion, whose volume increases to 80% of the total mitochondrial volume, and reorganizes into a cage-like structure encompassing first the mitotic spindle and then the entire cytokinetic apparatus. During cytokinesis, the cage-like mitochondrion divides into two independent tentacular mitochondria from which new, small mitochondria arise by fission. These cell cycle-dependent changes in mitochondrial architecture explain how these meristematic cells can achieve a high rate of mtDNA recombination and ensure the even partitioning of mitochondria between daughter cells.
Information and ICT in Microenterprises: Case of Malawi

This paper presents an assessment of analytical and functional roles of information and ICT on the livelihoods of microenterprises in context of a developing country. Six cases of microenterprises were analysed. Data was collected using semi-structured interviews and observations. The results confirmed that ICT supports better access to information for decision making on the livelihoods of microenterprises. However, microenterprises experienced challenges which inhibit their application of ICT in business activities. The main problems were lack of resources and access to ICTs. The study suggest the importance of understanding of the roles of information and ICTs so that appropriate solutions can be developed to mitigate some of the challenges faced by microenterprises and make them more sustainable.
A model calculation of coherence effects in the elastic backscattering of very low energy electrons (1–20 eV) from amorphous ice

Abstract Purpose: Backscattering of very low energy electrons in thin layers of amorphous ice is known to provide experimental data for the elastic and inelastic cross sections and indicates values to be expected in liquid water. The extraction of cross sections was based on a transport analysis consistent with Monte Carlo simulation of electron trajectories. However, at electron energies below 20 eV, quantum coherence effects may be important and trajectory-based methods may be in significant error. This possibility is here investigated by calculating quantum multiple elastic scattering of electrons in a simple model of a very small, thin foil of amorphous ice. Method: The average quantum multiple elastic scattering of electrons is calculated for a large number of simulated foils, using a point-scatterer model for the water molecule and taking inelastic absorption into account. The calculation is compared with a corresponding trajectory simulation. Results: The difference between average quantum scattering and trajectory simulation at energies below about 20 eV is large, in particular in the forward scattering direction, and is found to be almost entirely due to coherence effects associated with the short-range order in the amorphous ice. For electrons backscattered at the experimental detection angle (45° relative to the surface normal) the difference is however small except at electron energies below about 10 eV. Conclusion: Although coherence effects are in general found to be strong, the mean free path values derived by trajectory-based analysis may actually be in fair agreement with the result of an analysis based on quantum scattering, at least for electron energies larger than about 10 eV.