Miracle-dz/UniFAR-FTUs huggingface dataset:
De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms

Nypa fruticans (Arecaceae) is the only monocot species of true mangroves. This species represents the earliest mangrove fossil recorded. How N. fruticans adapts to the harsh and unstable intertidal zone is an interesting question. However, the 60 gene segments deposited in NCBI are insufficient for solving this question. In this study, we sequenced, assembled and annotated the transcriptome of N. fruticans using next-generation sequencing technology. A total of 19,918,800 clean paired-end reads were de novo assembled into 45,368 unigenes with a N50 length of 1,096 bp. A total of 41.35% unigenes were functionally annotated using Blast2GO. Many genes annotated to “response to stress” and 15 putative positively selected genes were identified. Simple sequence repeats were identified and compared with other palms. The divergence time between N. fruticans and other palms was estimated at 75 million years ago using the genomic data, which is consistent with the fossil record. After calculating the synonymous substitution rate between paralogs, we found that two whole-genome duplication events were shared by N. fruticans and other palms. These duplication events provided a large amount of raw material for the more than 2,000 later speciation events in Arecaceae. This study provides a high quality resource for further functional and evolutionary studies of N. fruticans and palms in general.
Parsing as Deduction

By exploring the relationship between parsing and deduction, a new and more general view of chart parsing is obtained, which encompasses parsing for grammar formalisms based on unification, and is the basis of the Earley Deduction proof procedure for definite clauses. The efficiency of this approach for an interesting class of grammars is discussed.
Nuclear factor-kappa B pathway and response in a phase II trial of bortezomib and docetaxel in patients with recurrent and/or metastatic head and neck squamous cell carcinoma.

BACKGROUND Our previous study has shown that nuclear factor-kappa B (NF-kappaB)-signaling pathway was associated with a higher rate of recurrence in head and neck squamous cell carcinoma (HNSCC). The combination of bortezomib, an NF-kappaB inhibitor by inhibition of proteasomes, plus docetaxel was assessed for efficacy and toxicity. MATERIALS AND METHODS Patients with recurrent and/or metastatic HNSCC were enrolled on a phase II bortezomib/docetaxel trial (bortezomib 1.6 mg/m(2) and docetaxel 40 mg/m(2) on days 1 and 8 of a 21-day cycle). Response was assessed using RECIST. Tissue specimens were evaluated for the presence of human papillomavirus (HPV) and expression of NF-kappaB-associated genes. RESULTS Twenty-one of 25 enrolled patients were assessable for response; one partial response (PR, 5%), 10 stable disease (SD, 48%) and 10 progressive disease (PD, 48%). Patients with PR/SD had significantly longer survival compared with patients with PD and the regimen was well tolerated. Only one of 20 tumors was positive for HPV. Patients with PD had higher expression of NF-kappaB and epidermal growth factor receptor-associated genes in their tumors by gene expression analysis. CONCLUSION Further understanding of treatment resistance and interactions between bortezomib and docetaxel may provide novel approaches in managing HNSCC.
Structure of Vegetables Farming and Farmer’s Perception of Soil and Water Degradation in Two Periurban Areas in Yaounde Cameroon

Vegetable farming is an activity sensitive to the dynamism of the population and to the level of intensification in the use of soil resources. A study was conducted in the peri-urban zones of Yaounde to present the socioeconomic characteristics of vegetable farming and the farmers’ perception of soil and water degradation as a result of this activity. A semi-structured questionnaire was administered to this purpose in 2016 in two vegetable farming sites in Yaounde, namely Nkolbisson and Nkolondom III. Results showed that most vegetable farmers from both sites (around 75%) lack training in agriculture while 74 and 90 didn’t benefit from training on management of pesticides. Spreading and landfilling of amendments are the two most popular ways of applying fertilizers. In fact, while the majority (35.4%) of these fertilizers is applied at planting time, the minority (4.9%) is applied several months before planting. Besides young plots are more exploited (52.4% and 30%) compared to older ones (2.4% and 5%) in Nkolondom III and Nkolbisson respectively, as they are more responsive to fertilizer application. As consequence, high rates of fertilizers are applied to the oldest farms. As for irrigation water, it is altogether polluted. Base on the above, the farmers’ perception of degradation is seen through the degradation of soils properties with time in the order of 14.3% to 60% and 15% to 44% at Nkolbisson and Nkolondom III respectively resulting in a gradual decrease of crop production (up to 50%). It is also seen through the polluted produce obtained from irrigation and cleaning water.
Structural Biology and Crystallization Communications Crystallization and Preliminary X-ray Diffraction Analyses of Several Forms of the Cfab Major Subunit of Enterotoxigenic Escherichia Coli Cfa/i Fimbriae

Enterotoxigenic Escherichia coli (ETEC), a major global cause of diarrhea, initiates the pathogenic process via fimbriae-mediated attachment to the small intestinal epithelium. A common prototypic ETEC fimbria, colonization factor antigen I (CFA/I), consists of a tip-localized minor adhesive subunit CfaE and the stalk-forming major subunit CfaB, both of which are necessary for fimbrial assembly. To elucidate the structure of CFA/I at atomic resolution, three recom-binant proteins were generated consisting of fusions of the minor and major subunits (CfaEB) and of two (CfaBB) and three (CfaBBB) repeats of the major subunit. Crystals of CfaEB diffracted X-rays to 2.1 A ˚ resolution and displayed the symmetry of space group P2 1. CfaBB exhibited a crystal diffraction limit of 2.3 A ˚ resolution and had the symmetry of space group P2 1 2 1 2. CfaBBB crystallized in the monoclinic space group C2 and diffracted X-rays to 2.3 A ˚ resolution. These structures were determined using the molecular-replacement method.
Clinical Outcome After First and Recurrent Hemorrhage in Patients With Untreated Brain Arteriovenous Malformation

Background and Purpose— The morbidity from spontaneous hemorrhage of untreated brain arteriovenous malformations (AVM) is not well described. Methods— The 241 consecutive AVM patients (mean age 37±16 years, 52% women) from the prospective Columbia AVM Databank initially presenting with hemorrhage were evaluated using the Rankin Scale (RS) and the National Institute of Health Stroke Scale (NIHSS). From the 241 AVM patients, 29 (12%) had subsequent intracranial hemorrhage during follow-up. For further comparisons, 84 non-AVM patients with intracerebral hemorrhage from the Northern Manhattan Study (NOMAS) served as a control group. Results— In 241 AVM patients presenting with hemorrhage the median RS was 2 and the median NIHSS was 1 (49% RS 0 to 1, 61% NIHSS <2). The median time between hemorrhage and clinical evaluation was 11 days (mean 219 days). Recurrent AVM hemorrhage during follow-up resulted in no significant increase in morbidity (median RS 2, P=0.004; median NIHSS 3, P=0.322; time between hemorrhage and study evaluation: median 55 days, mean 657 days). Among AVM-hemorrhage subtypes, parenchymatous AVM hemorrhage was associated with higher stroke morbidity (odds ratio, 2.9; 95% CI, 1.5 to 5.8 for NIHSS ≥2) than nonparenchymatous hemorrhages. Parenchymatous AVM hemorrhage had a significantly better outcome (median NIHSS 1) than non-AVM related hemorrhage (median NIHSS 12; P<0.0001). Conclusions— Hemorrhage, either at initial presentation or during follow-up of untreated AVM patients appears to carry a lower morbidity than intracranial hemorrhage from other causes. These findings support a careful weighing of risks from interventional treatment and natural history.
Rituximab for refractory granulomatosis with polyangiitis (Wegener's granulomatosis): comparison of efficacy in granulomatous versus vasculitic manifestations

Objective First, to investigate the overall efficacy and safety of rituximab (RTX) in refractory granulomatosis with polyangiitis (GPA) in a tertiary referral centre. Second, to compare the efficacy of RTX in granulomatous and vasculitic manifestations in GPA. Patients and methods This study comprised a retrospective, standardised data collection from all patients who received RTX for refractory Wegener's granulomatosis from 2002 to 2010. Patients were assessed by a standardised interdisciplinary diagnostic procedure (including ear, nose and throat and ophthalmology assessment, MRI, immunodiagnostics, B-cell levels and Birmingham Vasculitis Activity Score) and were treated by standardised therapeutic regimens according to available evidence. Results 59 patients received 75 cycles of RTX. 9.3% achieved complete remission. A response was documented in 61.3% (improvement in 52%, unchanged disease activity in 9.3%), 26.7% had refractory disease. Birmingham Vasculitis Activity Score, disease extent index, erythrocyte sedimentation rate, C-reactive protein and prednisolone demand decreased significantly. All patients achieved B-cell depletion. Granulomatous manifestations such as orbital granuloma and pachymeningitis were more frequently refractory to RTX than vasculitis or other granulomatous manifestations. Thus, for example, complete remission/improvement was found in 89.2% of patients with renal disease and in only 44.4% of those with orbital masses (p=0.003). The relapse rate was 44.4% after a median period of 13.5 months. Adverse events occurred in 29%, pneumonia in 15% and death in 3%. Conclusion The overall response rate of refractory GPA to RTX was high (61.3% complete remission or improvement). Response rates of vasculitic manifestations were excellent; failure of response/progress was mostly due to granulomatous manifestations, especially orbital masses. Relapse rates were high (40%) despite maintenance treatment.
Use of Self-Selected Postures to Regulate Multi-Joint Stiffness During Unconstrained Tasks

Background The human motor system is highly redundant, having more kinematic degrees of freedom than necessary to complete a given task. Understanding how kinematic redundancies are utilized in different tasks remains a fundamental question in motor control. One possibility is that they can be used to tune the mechanical properties of a limb to the specific requirements of a task. For example, many tasks such as tool usage compromise arm stability along specific directions. These tasks only can be completed if the nervous system adapts the mechanical properties of the arm such that the arm, coupled to the tool, remains stable. The purpose of this study was to determine if posture selection is a critical component of endpoint stiffness regulation during unconstrained tasks. Methodology/Principal Findings Three-dimensional (3D) estimates of endpoint stiffness were used to quantify limb mechanics. Most previous studies examining endpoint stiffness adaptation were completed in 2D using constrained postures to maintain a non-redundant mapping between joint angles and hand location. Our hypothesis was that during unconstrained conditions, subjects would select arm postures that matched endpoint stiffness to the functional requirements of the task. The hypothesis was tested during endpoint tracking tasks in which subjects interacted with unstable haptic environments, simulated using a 3D robotic manipulator. We found that arm posture had a significant effect on endpoint tracking accuracy and that subjects selected postures that improved tracking performance. For environments in which arm posture had a large effect on tracking accuracy, the self-selected postures oriented the direction of maximal endpoint stiffness towards the direction of the unstable haptic environment. Conclusions/Significance These results demonstrate how changes in arm posture can have a dramatic effect on task performance and suggest that postural selection is a fundamental mechanism by which kinematic redundancies can be exploited to regulate arm stiffness in unconstrained tasks.
Genetic introgression of ethylene-suppressed transgenic tomatoes with higher-polyamines trait overcomes many unintended effects due to reduced ethylene on the primary metabolome

Ethylene regulates a myriad physiological and biochemical processes in ripening fruits and is accepted as the ripening hormone for the climacteric fruits. However, its effects on metabolome and resulting fruit quality are not yet fully understood, particularly when some of the ripening-associated biochemical changes are independent of ethylene action. We have generated a homozygous transgenic tomato genotype (2AS-AS) that exhibits reduced ethylene production as a result of impaired expression of 1-aminocyclopropane-1-carboxylate synthase 2 gene by its antisense RNA and had a longer shelf life. Double transgenic hybrid (2AS-AS × 579HO) developed through a genetic cross between 2AS-AS and 579HO (Mehta et al., 2002) lines resulted in significantly higher ethylene production than either the WT or 2AS-AS fruit. To determine the effects of reduced ethylene and introgression of higher polyamines’ trait, the metabolic profiles of ripening fruits from WT (556AZ), 2AS-AS, and 2AS-AS × 579HO lines were determined using 1H-NMR spectroscopy. The levels of Glu, Asp, AMP, Adenosine, Nucl1, and Nucl2 increased during ripening of the WT fruit. The increases in Glu, Asp, and AMP levels were attenuated in 2AS-AS fruit but recovered in the double hybrid with higher ethylene and polyamine levels. The ripening-associated decreases in Ala, Tyr, Val, Ile, Phe, malate, and myo-inositol levels in the 2AS-AS line were not reversed in the double hybrid line suggesting a developmental/ripening regulated accumulation of these metabolites independent of ethylene. Significant increases in the levels of fumarate, formate, choline, Nucl1, and Nucl2 at most stages of ripening fruit were found in the double transgenic line due to introgression with higher-polyamines trait. Taken together these results show that the ripening-associated metabolic changes are both ethylene dependent and independent, and that the fruit metabolome is under the control of multiple regulators, including ethylene and polyamines.
Investigating Effect of Growth Promoting Bacteria and Nitrogen Fertilizer on Qualitative and Quantitative Traits of Zea Mays L. Hybrids

Fertilizer management plays an important role in obtaining satisfactory yields from maize. In addition, fertilizer management is essential for achieving sustainable agriculture and protecting the environment. This research was conducted by split plot experiment based on randomized complete block design with four replications. Main factor was integrated with chemical and biological fertilizers in four levels that included 100, 75, 50, 25% quantities of nitrogen and phosphorus chemical fertilizers and with zero and 100% of biological fertilizers. Sub factor was three types of maize hybrids including Single cross 704, Single cross Karon 701 (SLD 45/1/2-1× MO17), Single cross Mobin (SLD 45/1/2-1× SLH 2/29/14/2-4/1). Analysis of variance indicated effect of fertilizer on all measured traits instead seed oil percentage and chlorophyll index was significant but effect of hybrids on all traits instead seed protein percentage was not significant. Interaction effect of treatments on seed yield, seed protein percentage and seed oil percentage was significant at 5% and 1% probability level, respectively. According result of mean comparison effect of different level of fertilizer treatment of 50% chemical fertilizer + 100% bio-fertilizer had highest amount of Biological yield (26.49 t.ha-1), harvest index (56.71%), protein yield (1.19 t.ha-1), oil yield (1.18 t.ha-1), and chlorophyll index (53.04), although hybrid SC.704 by 50% Chemical fertilizer + 100% bio-fertilizer had higher seed yield (15.14 t.ha-1), seed protein percentage (9.98%) and seed oil percentage (9.48%). Finally according result of this research use up biological fertilizers with half the recommended amount of chemical fertilizers is the greatest help towards sustainable agriculture.
IFN-γ Mediates Enhancement of HIV Replication in Astrocytes by Inducing an Antagonist of the β-Catenin Pathway (DKK1) in a STAT 3-Dependent Manner

Typically, IFN-γ is an antiviral cytokine that inhibits the replication of many viruses, including HIV. However, in the CNS, IFN-γ induces HIV-productive replication in astrocytes. Although astrocytes in vitro are refractory to HIV replication, recent in vivo evidence demonstrated that astrocytes are infected by HIV, and their degree of infection is correlated with proximity to activated macrophages/microglia. The ability of IFN-γ to induce HIV replication in astrocytes suggests that the environmental milieu is critical in regulating the permissiveness of astrocytes to HIV infection. We evaluated the mechanism by which IFN-γ relieves restricted HIV replication in astrocytes. We demonstrate that although astrocytes have robust endogenous β-catenin signaling, a pathway that is a potent inhibitor of HIV replication, IFN-γ diminished β-catenin signaling in astrocytes by 40%, as evaluated by both active β-catenin protein expression and β-catenin-mediated T cell factor/lymphoid enhancer reporter (TOPflash) activity. Further, IFN-γ–mediated inhibition of β-catenin signaling was dependent on its ability to induce an antagonist of the β-catenin signaling pathway, Dickkopf-related protein 1, in a STAT 3-dependent manner. Inhibition of STAT3 and Dickkopf-related protein 1 abrogated the ability of IFN-γ to enhance HIV replication in astrocytes. These data demonstrated that IFN-γ induces HIV replication in astrocytes by antagonizing the β-catenin pathway. To our knowledge, this is the first report to point to an intricate cross-talk between IFN-γ signaling and β-catenin signaling that may have biologic and virologic effects on HIV outcome in the CNS, as well as on broader processes where the two pathways interface.
Difference limen for formant frequency discrimination at high fundamental frequencies

In previous studies of formant frequency discrimination, variation in the stimuli has mainly concerned the formant frequencies while other factors which may affect formant frequency discrimination have largely been ignored. In most studies, fundamental frequencies typical of adult male speakers have been used. In the study presented here, formant frequency discrimination as a function of fundamental frequency level was studied. Contrary to expectations, fundamental frequency level did not seem to affect formant frequency discrimination. This was true even when the fundamental frequency was higher than the tested formant frequency. The implication of these findings is that formant frequency discrimination must, at least partly, rely on some other mechanism than reconstruction of the vocal tract transfer function. It is suggested that listeners use differences in the amplitude of partials to discriminate between complex vowel like sounds. Asymmetries in the distribution of these amplitudes may also explain the corresponding asymmetries found in perception.
Why individuals switch to using mobile payment: A migration-theoretic, empirical study

With mobile payment, individuals can buy goods and services through the use of a mobile device and wireless technology. Still, although the usage of mobile payment provides several advantages, such as a more convenient and faster paying-process, it is hardly used. Individuals rather stick with their current payment method, such as cash, EC card or credit card. In this study, we therefore try to find out, what factors would bring individuals to switch from their current payment method to mobile payment. We rely on the pull-push-mooring framework to depict the migration process from the current payment method to mobile payment. The results prove that dissatisfaction with the current payment method has a rather low influence on the intention to switch to mobile payment in comparison with other factors such as perceived usefulness or alternative attractiveness. Furthermore, switching costs have a negative influence on the intention to switch to mobile payment.
Cross-domain sentiment classification using a two-stage method

In this paper, we give out a two-stage approach for domain adaptation problem in sentiment classification. In the first stage, based on our observation that customers often use different words to comment on the similar topics in the different domains, we regard these common topics as the bridge to link the different domain-specific features. We propose a novel topic model named Transfer-PLSA to extract the topic knowledge between different domains. Through these common topics, the features in the source domain are corresponded to the target features, so that those domain-specific knowledge can be transferred across different domains. In the second step, we use the classifier trained on the labeled examples in the source domain to pick up some informative examples in the target domain. Then we retrain the classifier on these selected examples, so that the classifier is adapted for the target domain. Experimental results on sentiment classification in four different domains indicate that our method outperforms other traditional methods.
Full activity of the deleted in liver cancer 1 (DLC1) tumor suppressor depends on an LD-like motif that binds talin and focal adhesion kinase (FAK)

The deleted in liver cancer 1 (DLC1) tumor suppressor gene, which is frequently inactivated in cancer, encodes a Rho-GAP (GTPase activating protein) focal adhesion protein whose negative regulation of Rho-GTPases is necessary but not sufficient for its full tumor suppressor activity. Here, we report that DLC1 forms a complex with two prooncogenic focal adhesion proteins, talin and the focal adhesion kinase (FAK). We identified an 8-aa sequence (residues 469LDDILYHV476) in DLC1 and designated it an LD-like motif, because it shares homology with the LD motifs of paxillin. This motif was necessary for DLC1 binding to talin and FAK, because a DLC1 mutant, from which six of the residues have been deleted, and another mutant carrying amino acid substitutions in three of the residues are deficient for binding both proteins and localization of DLC1 to focal adhesions. FAK binding was independent of talin and vice versa. In bioassays, both DLC1 mutants were less active than wild-type (WT) DLC1, although the ability of the mutants to negatively regulate overall Rho-GTP was not impaired. We conclude that the LD-like motif, which binds talin and FAK, is required for the full tumor suppressor activity of DLC1 and contributes to the association of DLC1 with focal adhesions.