Miracle-dz/UniFAR-FTUs huggingface dataset:
Issues Relevant to the Adoption and Modification of Hospital Infection-Control Recommendations for Avian Influenza (H5N1 Infection) in Developing Countries

Abstract The reemergence of avian influenza (H5N1 infection) has heightened concern for a potential human influenza pandemic. Recommendations regarding preparation for a global avian influenza pandemic are available, and it is imperative that health care workers participate in preparedness planning and training. In developing countries, health care worker preparedness training should address the modes of avian influenza transmission and specify how to implement appropriate infection-control strategies to prevent and control the spread of avian influenza. We provide evidence for avian influenza transmission methods and identify prevention strategies relevant to infection control for hospitals in developing countries. Pandemic influenza preparedness plans must include health care administrative support, mechanisms to rapidly create temporary isolation facilities, systems to restrict access to exposed health care workers, and plans to involve specialists to screen and identify cases early, to provide for continuous monitoring to ensure adherence to optimal infection-control practices, and to provide regular feedback to health care workers
Exponential Stabilization of Boundary Controlled Port-Hamiltonian Systems With Dynamic Feedback

It is shown that a strictly-input passive linear finite dimensional controller exponentially stabilizes a large class of partial differential equations actuated at the boundary of a one dimensional spatial domain. This follows since the controller imposes exponential dissipation of the total energy. The result can by use for control synthesis and for the stability analysis of complex systems modeled by sets of coupled PDE's and ODE's. The result is specialized to port-Hamiltonian control systems and a simplified DNA-manipulation process is used to illustrate the result.
Natural Variation in Arabidopsis thaliana Revealed a Genetic Network Controlling Germination Under Salt Stress

Plant responses to environmental stresses are polygenic and complex traits. In this study quantitative genetics using natural variation in Arabidopsis thaliana was used to investigate the genetic architecture of plant responses to salt stress. Eighty seven A. thaliana accessions were screened and showed a large variation for root development and seed germination under 125 and 200 mM NaCl, respectively. Twenty two quantitative trait loci for these traits have been detected by phenotyping two recombinants inbred line populations, Sha x Col and Sha x Ler. Four QTLs controlling germination under salt were detected in the Sha x Col population. Interestingly, only one allelic combination at these four QTLs inhibits germination under salt stress, implying strong epistatic interactions between them. In this interacting context, we confirmed the effect of one QTL by phenotyping selected heterozygous inbred families. We also showed that this QTL is involved in the control of germination under other stress conditions such as KCl, mannitol, cold, glucose and ABA. Our data highlights the presence of a genetic network which consists of four interacting QTLs and controls germination under limiting environmental conditions.
The response regulator Npun_F1278 is essential for scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme ATCC 29133

Following exposure to long‐wavelength ultraviolet radiation (UVA), some cyanobacteria produce the indole‐alkaloid sunscreen scytonemin. The genomic region associated with scytonemin biosynthesis in the cyanobacterium Nostoc punctiforme includes 18 cotranscribed genes. A two‐component regulatory system (Npun_F1277/Npun_F1278) directly upstream from the biosynthetic genes was identified through comparative genomics and is likely involved in scytonemin regulation. In this study, the response regulator (RR), Npun_F1278, was evaluated for its ability to regulate scytonemin biosynthesis using a mutant strain of N. punctiforme deficient in this gene, hereafter strain Δ1278. Following UVA radiation, the typical stimulus to initiate scytonemin biosynthesis, Δ1278 was incapable of producing scytonemin. A phenotypic characterization of Δ1278 suggests that aside from the ability to produce scytonemin, the deletion of the Npun_F1278 gene does not affect the cellular morphology, cellular differentiation capability, or lipid‐soluble pigment complement of Δ1278 compared to the wildtype. The mutant, however, had a slower specific growth rate under white light and produced ~2.5‐fold more phycocyanin per cell under UVA than the wildtype. Since Δ1278 does not produce scytonemin, this study demonstrates that the RR gene, Npun_F1278, is essential for scytonemin biosynthesis in N. punctiforme. While most of the evaluated effects of this gene appear to be specific for scytonemin, this regulator may also influence the overall health of the cell and phycobiliprotein synthesis, directly or indirectly. This is the first study to identify a regulatory gene involved in the biosynthesis of the sunscreen scytonemin and posits a link between cell growth, pigment synthesis, and sunscreen production.
Posttraumatic Stress Disorder and Psychiatric Comorbidity Following the 2010 Flood in Pakistan: Exposure Characteristics, Cognitive Distortions, and Emotional Suppression

This study investigated the extent of posttraumatic stress disorder (PTSD) and psychiatric comorbidity among the 2010 flood victims in Pakistan and its relationship with disaster exposure characteristics, cognitive distortions, and emotional suppression. One hundred and thirty-one (F = 89, M = 42) flood victims were assessed using the Posttraumatic Diagnostic Scale, the General Health Questionnaire-28, the Cognitive Distortion Scales, and the Courtauld Emotional Control Scale. The results showed that all victims met the diagnostic criteria for PTSD and scored above the cut-off for psychiatric caseness. Partial least squares modelling showed that disaster exposure characteristics were significantly correlated with PTSD and psychiatric comorbidity. Disaster exposure characteristics were also significantly associated with cognitive distortions which in turn were also significantly associated with PTSD and psychiatric comorbidity. Cognitive distortions were also correlated with emotional suppression which, however, was not associated with PTSD or psychiatric comorbidity. To conclude, the flood victims reported PTSD and psychiatric comorbid symptoms which were related to their subjective exposure to the flood. Such exposure led to the development of dysfunctional thinking patterns which in turn influenced distress symptoms.
Corneal Biomechanical Changes and Tissue Remodeling After SMILE and LASIK.

Purpose To evaluate transient corneal tissue healing and biomechanical changes between laser in situ keratomileusis (LASIK) and small incision lenticule extraction (SMILE) eyes. Methods In each patient, one eye underwent LASIK and the other underwent SMILE. Optical coherence tomography (OCT) and dynamic Scheimpflug imaging (Corvis-ST) was used to assess tissue healing and biomechanics, respectively. Analyses of OCT scans yielded corneal speckle distribution (CSD) and Bowman's roughness index (BRI). Waveform analyses of deformation amplitude yielded corneal stiffness. Further, corneal force versus corneal deformation data helped compare the two procedures. Results BRI increased and then decreased transiently after both treatments (P < 0.05). However, SMILE eyes had BRI similar to that of their preoperative state compared to LASIK eyes at 6-month follow-up. CSD indicated a marked increase in the number of bright pixels and a decrease in the number of dark pixels after SMILE (1-month follow-up) and LASIK eyes (3-month follow-up), respectively. CSD returned to near preoperative state thereafter, respectively. Corneal stiffness change from preoperative state was similar between LASIK and SMILE eyes. However, deformation at discrete values of corneal force indicated some recovery of biomechanical strength after SMILE, but not in LASIK eyes. Conclusions BRI and CSD indicated earlier tissue healing in SMILE eyes than in LASIK. CSD results may indicate delayed cell death in LASIK eyes and increased light scatter due to interface fluid in SMILE eyes. Corneal biomechanical strength remodeled better in SMILE. This may indicate some hydration-related recovery.
Comparison of intranasal and transdermal estradiol on nasal mucosa in postmenopausal women

Objective:To compare nasal symptomatology and function and local concentrations of estradiol (E2), estradiol receptor (ER&agr;), vasoactive intestinal peptide (VIP), substance P (SP) and neuropeptide Y (NPY) in nasal biopsies of 20 postmenopausal women complaining of paradoxical nasal stuffiness before and after treatment with intranasal or transdermal E2. Design:Twenty healthy postmenopausal women willing to start hormone therapy (HT) were allocated to one of two groups, using a computer-generated randomization list.Ten postmenopausal women were treated with transdermal 17β-estradiol 50 μg daily plus nomegestrole acetate 5 mg/day for 12 days per 28-day cycle for 6 months (Group A). Ten postmenopausal women were treated with intranasal 17β-estradiol 300 μg/day (one spray delivery of 150 μg per nostril) plus nomegestrole acetate 5 mg/day for 12 days per 28-day cycle for 6 months (Group B). Fourteen fertile women undergoing nasal mucosa biopsy during plastic surgery were used as controls for the immunohistochemical evaluation (Group C). All women in groups A and B underwent evaluation of nasal stuffiness score, mucociliary transport time, rhinoscopy, and active anterior rhinomanometry at the beginning of the study and after, VIP, SP, and 6 months of HT. Nasal biopsies and evaluation of local concentrations of E2, ER&agr; NPY were performed in groups A and B before and after 6 months of HT and in group C. Results:Both intranasal and transdermal HT improve nasal symptomatology and nasal mucosa appearance and reduce mean mucociliary transport time. The effectiveness of intranasally administered therapy at improving nasal function is significantly better than transdermal therapy. In comparison with premenopausal controls, untreated postmenopausal women of group A and B showed significantly decreased immunopositivity for E2, ER&agr;, and SP. HT induced a significant increase in E2, ER&agr;, VIP, and SP and a decrease in NPY immunopositivity. Intranasal therapy was associated with a significantly higher immunopositivity for VIP and SP. Conclusions:HT improves nasal function and symptomatology in postmenopausal women with paradoxical nasal stuffiness, modulating nasal mucosa function through an action on cholinergic, adrenergic, and sensory peptides. Intranasally administered HT is more effective at improving nasal function than transdermal HT.
Peeling Plaids Apart: Context Counteracts Cross-Orientation Contrast Masking

Background Contrast discrimination for an image is usually harder if another image is superimposed on top. We asked whether such contrast masking may be enhanced or relieved depending on cues promoting integration of both images as a single pattern, versus segmentation into two independent components. Methodology & Principal Findings Contrast discrimination thresholds for a foveal test grating were sharply elevated in the presence of a perfectly overlapping orthogonally-oriented mask grating. However thresholds returned to the unmasked baseline when a surround grating was added, having the same orientation and phase of either the test or mask grating. Both such masking and ‘unmasking’ effects were much stronger for moving than static stimuli. Conclusions & Significance Our results suggest that common-fate motion reinforces the perception of a single coherent plaid pattern, while the surround helps to identify each component independently, thus peeling the plaid apart again. These results challenge current models of early vision, suggesting that higher-level surface organization influences contrast encoding, determining whether the contrast of a grating may be recovered independently from that of its mask.
The adenovirus E3 10.4K and 14.5K proteins, which function to prevent cytolysis by tumor necrosis factor and to down-regulate the epidermal growth factor receptor, are localized in the plasma membrane

The adenovirus type 2 and 5 E3 10,400- and 14,500-molecular-weight (10.4K and 14.5K) proteins are both required to protect some cell lines from lysis by tumor necrosis factor and to down-regulate the epidermal growth factor receptor. We have shown previously that both 10.4K and 14.5K are integral membrane proteins and that 14.5K is phosphorylated and O glycosylated. The 10.4K protein coimmunoprecipitates with 14.5K, indicating that the two proteins function as a complex. Here we show, using immunofluorescence and two different cell surface-labeling techniques, that both proteins are localized in the plasma membrane. In addition, we show that trafficking of each protein to the plasma membrane depends on concomitant expression of the other protein. Finally, neither protein could be immunoprecipitated from conditioned media, indicating that neither is secreted. Taken together, these results suggest that the plasma membrane is the site at which 10.4K and 14.5K function to inhibit cytolysis by tumor necrosis factor and to down-regulate the epidermal growth factor receptor.
Towards Probabilistic Acceptors and Transducers for Feature Structures

Weighted finite-state acceptors and transducers (Pereira and Riley, 1997) are a critical technology for NLP and speech systems. They flexibly capture many kinds of stateful left-to-right substitution, simple transducers can be composed into more complex ones, and they are EM- trainable. They are unable to handle long-range syntactic movement, but tree acceptors and transducers address this weakness (Knight and Graehl, 2005). Tree automata have been profitably used in syntax-based MT systems. Still, strings and trees are both weak at representing linguistic structure involving semantics and reference ("who did what to whom"). Feature structures provide an attractive, well-studied, standard format (Shieber, 1986; Rounds and Kasper, 1986), which we can view computationally as directed acyclic graphs. In this paper, we develop probabilistic acceptors and transducers for feature structures, demonstrate them on linguistic problems, and lay down a foundation for semantics-based MT.
Selective Enhancing Effect of Early Mitotic Inhibitor 1 (Emi1) Depletion on the Sensitivity of Doxorubicin or X-ray Treatment in Human Cancer Cells*

Background: To improve the effectiveness of chemo- and radiotherapy only in cancer tissue is important for avoiding side effects. Results: Emi1 depletion enhanced the sensitivity of anticancer reagents and X-ray irradiation in cancer cells. Conclusion: Emi1 siRNA would be a useful new modality for enhancing the effect of chemo- and radiotherapy in various tumors. Significance: This work provides new insights regarding synergistic effect of Emi1 knockdown in combination therapies. Chemotherapy and radiation in addition to surgery has proven useful in a number of different cancer types, but the effectiveness in normal tissue cannot be avoided in these therapies. To improve the effectiveness of these therapies selectively in cancer tissue is important for avoiding side effects. Early mitotic inhibitor 1 (Emi1) is known to have the function to inhibit anaphase-promoting complex/cyclosome ubiquitin ligase complex, which ubiquitylates the cell cycle-related proteins. It recently has been shown that Emi1 knockdown prevents transition from S to G2 phase by down-regulating geminin via anaphase-promoting complex/cyclosome activation. At present, anticancer drugs for targeting DNA synthesis to interfere with rapidly dividing cells commonly are used. As Emi1 depletion interferes with completion of DNA synthesis in cancer cells, we thought that Emi1 knockdown might enhance the sensitivity for anticancer agents. Here, we confirmed that Emi1 siRNA induced polyploidy for preventing transition from S to G2 phase in several cancer cell lines. Then, we treated Emi1 depleted cells with doxorubicin. Interestingly, increased apoptotic cells were observed after doxorubicin treatment in Emi1 siRNA-treated cancer cells. In addition, Emi1 depletion enhanced the sensitivity of x-ray irradiation in cancer cells. Importantly, synergistic effect of Emi1 knockdown in these combination therapies was not observed in normal cells. These results suggest that Emi1 siRNA can be a useful tool for enhancing of sensitivity of cancer cells to anticancer reagents and radiation.
Impact of Resveratrol on Glucose Control, Hippocampal Structure and Connectivity, and Memory Performance in Patients with Mild Cognitive Impairment

In healthy older adults, resveratrol supplementation has been shown to improve long-term glucose control, resting-state functional connectivity (RSFC) of the hippocampus, and memory function. Here, we aimed to investigate if these beneficial effects extend to individuals at high-risk for dementia, i.e., patients with mild cognitive impairment (MCI). In a randomized, double-blind interventional study, 40 well-characterized patients with MCI (21 females; 50–80 years) completed 26 weeks of resveratrol (200 mg/d; n = 18) or placebo (1,015 mg/d olive oil; n = 22) intake. Serum levels of glucose, glycated hemoglobin A1c and insulin were determined before and after intervention. Moreover, cerebral magnetic resonance imaging (MRI) (3T) (n = 14 vs. 16) was conducted to analyze hippocampus volume, microstructure and RSFC, and neuropsychological testing was conducted to assess learning and memory (primary endpoint) at both time points. In comparison to the control group, resveratrol supplementation resulted in lower glycated hemoglobin A1c concentration with a moderate effect size (ANOVARM p = 0.059, Cohen's d = 0.66), higher RSFC between right anterior hippocampus and right angular cortex (p < 0.001), and led to a moderate preservation of left anterior hippocampus volume (ANOVARM p = 0.061, Cohen's d = 0.68). No significant differences in memory performance emerged between groups. This proof-of-concept study indicates for the first-time that resveratrol intake may reduce glycated hemoglobin A1c, preserves hippocampus volume, and improves hippocampus RSFC in at-risk patients for dementia. Larger trials with longer intervention time should now determine if these benefits can be validated and extended to cognitive function.
ICML2011 Unsupervised and Transfer Learning Workshop

We organized a data mining challenge in "unsupervised and transfer learning" (the UTL challenge) followed by a workshop of the same name at the ICML 2011 conference in Bellevue, Washington. This introduction presents the highlights of the outstanding contributions that were made, which are regrouped in this issue of JMLR W&CP. Novel methodologies emerged to capitalize on large volumes of unlabeled data from tasks related (but different) from a target task, including a method to learn data kernels (similarity measures) and new deep architectures for feature learning.
Ribosome Binding to a 5′ Translational Enhancer Is Altered in the Presence of the 3′ Untranslated Region in Cap-Independent Translation of Turnip Crinkle Virus

ABSTRACT Plus-strand RNA viruses without 5′ caps require noncanonical mechanisms for ribosome recruitment. A translational enhancer in the 3′ untranslated region (UTR) of Turnip crinkle virus (TCV) contains an internal T-shaped structure (TSS) that binds to 60S ribosomal subunits. We now report that the 63-nucleotide (nt) 5′ UTR of TCV contains a 19-nt pyrimidine-rich element near the initiation codon that supports translation of an internal open reading frame (ORF) independent of upstream 5′ UTR sequences. Addition of 80S ribosomes to the 5′ UTR reduced the flexibility of the polypyrimidine residues and generated a toeprint consistent with binding to this region. Binding of salt-washed 40S ribosomal subunits was reduced 6-fold when the pyrimidine-rich sequence was mutated. 40S subunit binding generated the same toeprint as 80S ribosomes but also additional ones near the 5′ end. Generation of out-of-frame AUGs upstream of the polypyrimidine region reduced translation, which suggests that 5′-terminal entry of 40S subunits is followed by scanning and that the polypyrimidine region is needed for an alternative function that requires ribosome binding. No evidence for RNA-RNA interactions between 5′ and 3′ sequences was found, suggesting that TCV utilizes an alternative means for circularizing its genome. Combining 5′ and 3′ UTR fragments in vitro had no discernible effect on the structures of the RNAs. In contrast, when 80S ribosomes were added to both fragments, structural changes were found in the 5′ UTR polypyrimidine tract that were not evident when ribosomes interacted with the individual fragments. This suggests that ribosomes can promote an interaction between the 5′ and 3′ UTRs of TCV.
Functional cooperation of Dam1, Ipl1, and the inner centromere protein (INCENP)–related protein Sli15 during chromosome segregation

We have shown previously that Ipl1 and Sli15 are required for chromosome segregation in Saccharomyces cerevisiae. Sli15 associates directly with the Ipl1 protein kinase and these two proteins colocalize to the mitotic spindle. We show here that Sli15 stimulates the in vitro, and likely in vivo, kinase activity of Ipl1, and Sli15 facilitates the association of Ipl1 with the mitotic spindle. The Ipl1-binding and -stimulating activities of Sli15 both reside within a region containing homology to the metazoan inner centromere protein (INCENP). Ipl1 and Sli15 also bind to Dam1, a microtubule-binding protein required for mitotic spindle integrity and kinetochore function. Sli15 and Dam1 are most likely physiological targets of Ipl1 since Ipl1 can phosphorylate both proteins efficiently in vitro, and the in vivo phosphorylation of both proteins is reduced in ipl1 mutants. Some dam1 mutations exacerbate the phenotype of ipl1 and sli15 mutants, thus providing evidence that Dam1 interactions with Ipl1–Sli15 are functionally important in vivo. Similar to Dam1, Ipl1 and Sli15 each bind to microtubules directly in vitro, and they are associated with yeast centromeric DNA in vivo. Given their dual association with microtubules and kinetochores, Ipl1, Sli15, and Dam1 may play crucial roles in regulating chromosome–spindle interactions or in the movement of kinetochores along microtubules.