Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure‐Based Mutational Study of an Archaeal DNA Ligase towards Improvement of Ligation Activity

DNA ligases catalyze the joining of strand breaks in duplex DNA. The DNA ligase of Pyrococcus furiosus (PfuLig), which architecturally resembles the human DNA ligase I (hLigI), comprises an N‐terminal DNA‐binding domain, a middle adenylylation domain, and a C‐terminal oligonucleotide‐binding (OB)‐fold domain. Here we addressed the C‐terminal helix in the OB‐fold domain of PfuLig by mutational analysis. The crystal structure of PfuLig revealed that this helix stabilizes a closed conformation of the enzyme by forming several ionic interactions with the adenylylation domain. The C‐terminal helix is oriented differently in hLigI when DNA is bound; this suggested that disruption of its interaction with the adenylylation domain might facilitate the binding of DNA substrates. We indeed identified one of its residues, Asp540, as being critical for ligation efficiency. The D540R mutation improved the overall ligation activity relative to the wild‐type enzyme, and at lower temperatures; this is relevant to applications such as ligation amplification reactions. Physical and biochemical analyses indicated that the improved ligation activity of the D540R variant arises from effects on the ligase adenylylation step and on substrate DNA binding in particular.
Structure and Rules in Automated Multimedia Presentation Planning

During the planning of multimedia presentations, at least two distinct processes are required: planning the underlying discourse structure (that is, ordering and interrelating the information to be presented) and allocating the media (that is, delimiting the portions to be displayed by each individual medium). The former process has been the topic of several studies in the area of text planning, but numerous questions remain for the latter, including: What is the nature of the allocation process | what does it start with and what does it produce? What information does it depend on? How should the two processes be performed | sequentially, interleaved, or simultaneously? In this paper, we deene Discourse Structure and Presentation Structure and outline the kinds of information that media allocation rules must depend on, including, centrally, information about the discourse structure. We describe a prototype planning system that performs the information-to-media allocation, arguing that since media allocation rules depend on the characteristics of the information to be presented, they can only be applied once the overall discourse structure has been essentially planned out and the individual portions of information have become apparent. spent a research visit of six months at USC/ISI working on this project for her Master's degree. Views and conclusions contained in this report are the authors' and should not be interpreted as representing the oocial opinion or policy of DARPA, RL, the U.S. Government, or any person or agency connected with them. The automated creation of multimedia presentations contains a number of challenging and interesting problems. Given a collection of information to display, what is the nature of the process of designing a multimedia presentation? What information does the process start with and what does it produce? On what information are its decision criteria based? Borrowing from the conceptually related eld of automated text generation, one might consider starting with a text planner that performs the tasks of information selection and organization, and then add to that a process that allocates the information to speciic media for presentation. In fact, one may hope that a single planning mechanism rather like a text planner will perform all three these tasks simultaneously; after all, it is dealing with the same information in all cases. Unfortunately, this appealing idea is not feasible. We argue in this paper that such integration cannot work because since the information-to-medium allocation process depends upon the overall structure of the discourse, …
A man with purple toes.

1 Wisniewski KE, French JH, Rosen JF, Koslowski PB, Tenner M, Wisniewski HM. Basal ganglia calcification (BGC) in Down's syndrome. Another manifestation of premature aging. Ann NYAcad Sci 1982;396:179-89. 2 Jakab I. Basal ganglia calcification and psychosis in mongolism. Eur Neurol 1978;17:300-14. 3 Lowenthal A, De Deyn P. Striopallidodentate calcifications. In: Joseph AB, Young RR, eds. Movement disorders in neurology and neuropsychiatry. Oxford: Blackwell Scientific Publications, 1992; pp262-9. 4 Benda CE. The child with mongolisnm (congenzital acronmicria). New York: Grune & Stratton, 1960. 5 Murofushi K. Symmetrischer Pseudokalk in stammganglien and Grosshirnmark mit diskreter Leukencephalopathie bei Downschem syndrom. Neuropediatrie 1974;5: 103-8.
Compressive sensing with side information : analysis, measurements design and applications

Compressive sensing is a breakthrough technology in view of the fact that it enables the acquisition and reconstruction of certain signals with a number of measurements much lower than those dictated by the Shannon-Nyquist paradigm. It has also been recognised in the last few years that it is possible to improve compressive sensing systems by leveraging additional knowledge – so-called side information – that may be available about the signal of interest. The goal of this thesis is to investigate how to improve the acquisition and reconstruction process in compressive sensing systems in the presence of side information. In particular, by assuming that both the signal of interest and the side information obey a joint Gaussian mixture model (GMM), the thesis focuses on the analysis and the design of linear measurements for two different scenarios: i) the scenario where one wishes to design a linear projection matrix to capture the signal of interest; and ii) the scenario where one wishes to design a linear projection matrix to capture the side information. In both cases, we derive sufficient and (occasionally) necessary conditions on the number of measurements needed for the reliable reconstruction in the low-noise regime and we also derive linear measurement designs that are close to optimal. Numerical results are presented with synthetic data from both Gaussian and GMM distributions and with real world imaging data that confirm that analysis is well aligned with practice. We also showcase our measurement design scheme can lead to significant improvement on the application example associated with the reconstruction of high-resolution RGB images from gray scale images using low-resolution, compressive, hyperspectral measurements as side information.
Efficacy and safety of CT‐P13, a biosimilar of infliximab, in patients with inflammatory bowel disease: A retrospective multicenter study

The biosimilar of infliximab, CT‐P13, has recently been shown to be equivalent to infliximab in both efficacy and safety in the treatment of rheumatologic diseases. However, no data are available with respect to the drug's efficacy in patients with inflammatory bowel disease (IBD). We aimed to assess the efficacy and safety of CT‐P13 in IBD patients
Treatment of post-myocardial infarction depressive disorder

Both major and minor depressive disorder post-myocardial infarction (MI) are associated with an increased risk of all-cause mortality, cardiac mortality and new cardiovascular events. Post-MI depressive disorder predicts slow recovery and poor quality of life. This review attends to post-MI depressive disorder, its underlying mechanisms and options for and effects of treatment. Evidence has been found for several mechanisms to be involved in the pathophysiology, including hypothalamus–pituitary–adrenal axis activity, immune activity, polyunsaturated fatty acids, serotonin, platelet activation, type D personality and negative health behavior. Five leading randomized controlled trials are discussed, showing safety and efficacy of antidepressive treatment in post-MI patients. Effects on cardiac outcome remain unclear.
ERAP1 in ankylosing spondylitis: genetics, biology and pathogenetic role

Purpose of reviewEndoplasmic reticulum aminopeptidase 1 (ERAP1) is an aminopeptidase of the endoplasmic reticulum involved in trimming of peptides to their optimal size for binding to major histocompatibility complex class I molecules. Natural ERAP1 polymorphism resulting in altered enzymatic activity is associated with ankylosing spondylitis, an inflammatory disorder very strongly linked to HLA-B27. Recent findingsThis review will summarize recent advances in the genetics of ERAP1 association with this disease, in the molecular basis of ERAP1 function and in the mechanism of functional interaction between ERAP1 and HLA-B27. SummaryThe findings suggest that the pathogenetic role of ERAP1 in ankylosing spondylitis is due to allotype-dependent alterations of the HLA-B27 peptidome that affect the immunologic and other features of HLA-B27.
Inhibition of astroglial nuclear factor κB reduces inflammation and improves functional recovery after spinal cord injury

In the central nervous system (CNS), the transcription factor nuclear factor (NF)-κB is a key regulator of inflammation and secondary injury processes. After trauma or disease, the expression of NF-κB–dependent genes is highly activated, leading to both protective and detrimental effects on CNS recovery. We demonstrate that selective inactivation of astroglial NF-κB in transgenic mice expressing a dominant negative (dn) form of the inhibitor of κBα under the control of an astrocyte-specific promoter (glial fibrillary acidic protein [GFAP]–dn mice) leads to a dramatic improvement in functional recovery 8 wk after contusive spinal cord injury (SCI). Histologically, GFAP mice exhibit reduced lesion volume and substantially increased white matter preservation. In parallel, they show reduced expression of proinflammatory chemokines and cytokines, such as CXCL10, CCL2, and transforming growth factor–β2, and of chondroitin sulfate proteoglycans participating in the formation of the glial scar. We conclude that selective inhibition of NF-κB signaling in astrocytes results in protective effects after SCI and propose the NF-κB pathway as a possible new target for the development of therapeutic strategies for the treatment of SCI.
How and why teenagers use video chat

Teenagers are increasingly using video chat systems to communicate with others, however, little research has been conducted to explore how and why they use the technology. To better understand this design space, we present the results of a study of twenty teenagers and their use of video chat systems such as Skype, FaceTime, and Google Hangouts. Our results show that video chat plays an important role in helping teenagers socialize with their friends after school and on weekends where it allows them to see emotional reactions and participate in activities like shared homework sessions, show and tell, and performances over distance. Yet video chat is also used to engage in more private activities such as gossiping, flirting, and even the viewing of sexual acts. This presents an interesting design challenge of supporting teen use of video chat while mitigating privacy and parental concerns.
Eligibility and rate of treatment for recombinant tissue plasminogen activator in acute ischemic stroke using different criteria.

OBJECTIVES The rate of recombinant tissue plasminogen activator (rtPA) use for stroke is low among the Chinese-Taiwanese. The study objective was to determine if less restrictive exclusion criteria for rtPA would increase eligibility and the rate of treatment. METHODS This retrospective before-and-after study was conducted from 2006 to 2009. The authors compared stroke patients treated under the old rtPA exclusion criteria (January 2006 to December 2008) with those treated with less restrictive rtPA exclusion criteria (January to December 2009). Rates of eligibility and treatment and reasons for exclusion from rtPA between the two phases were assessed. RESULTS Of 461 eligible patients during the study period, 333 were evaluated by the old criteria and 128 were evaluated by the less restrictive criteria. Minor or improving stroke was the primary exclusion reason in both groups (194/333, 58% vs. 70/128, 55%). Eligibility for rtPA was increased in the less restrictive criteria (35/127, 27%, 95% confidence interval [CI] = 20% to 36%) compared to the old criteria (40/333, 12%, 95% CI = 8.7% to 16%; p = 0.0001). Fewer patients were excluded due to old age in the less restrictive criteria (0/128, 0%) compared to the old criteria (37/333, 11%; p = 0.0001). The rate of consent refusal increased in the less restrictive criteria (27/128, 21%, 95% CI = 14% to 29%) compared to the old criteria (23/333, 6.9%, 95% CI = 4.4% to 10%; p < 0.0001). Rate of rtPA treatment was unchanged between the less restrictive criteria (8/128, 6.3%, 95% CI = 2.7% to 12%) and the old criteria (17/333, 5.1%, 95% CI = 3% to 8%; p = 0.63). CONCLUSIONS Increasing eligibility for rtPA does not increase the rate of treatment, possibly due to the high symptomatic intracerebral hemorrhage rate among Chinese-Taiwanese, which is a major concern among emergency physicians (EPs), neurologists, and patients. Dealing with perceived safety issues of rtPA is crucial before the rate of treatment can be increased.
Scientific Hangman: Gamifying Scientific Evidence for General Public

Governmental and private funding for research in many fields has resulted in a significant body of scientific evidence. Scientific evidence or content is made available in the form of thousands of articles communicated via digital libraries. This evidence is principally used by researchers, students and on occasions for societal impact such as commercial exploitation and popular science communication. How can we gamify communicating a large amount of scientific evidence to the general public? This is the question that intrigues us. We present the game of Scientific Hangman, based on the traditional game of hangman, to communicate scientific research in a fun manner. The puzzles in our game are based on automatic summarization of scientific article abstracts. Players play the game in an attempt to guess a word given a clue such as a paper abstract. Our first prototype, was evaluated on a focus group at the Cancer Registry of Norway by communicating information from invitation letters in cervical cancer screening. We also evaluated a second prototype of the game to have feedback on design improvements resulted from the first prototype.
Blood pressure in early adolescence in the offspring of preeclamptic and normotensive pregnancies

Objective To compare blood pressure (BP) in adolescence (11–12 years) among the offspring of preeclamptic and normotensive pregnancies. Method SBP and DBP of 181 girls and boys born after pregnancies with preeclampsia were measured and compared with the BP of 356 age-matched girls and boys of normotensive pregnancies. The association of preeclampsia with later BP was adjusted for perinatal information, anthropometric factors at follow-up, and maternal BP and BMI. Results In the preeclampsia group, SBP in early adolescence was higher than in the normotensive group (115.3 vs. 113.5 mmHg, P = 0.03), but there was no difference in DBP (66.4 vs. 65.3 mmHg, P = 0.10). After adjustment for maternal body mass and BP, the difference in SBP was largely attenuated. Conclusion The higher SBP among adolescent offspring of preeclamptic pregnancies could be mediated by maternal body mass or BP, factors that are positively associated with the risk of preeclampsia in pregnancy.
Palmitoleic Acid Improves Metabolic Functions in Fatty Liver by PPARα‐Dependent AMPK Activation

Background: Palmitoleic acid, since described as lipokine, increases glucose uptake by modulation of 5′AMP‐activated protein kinase (AMPK), as well as increasing lipolysis by activation of peroxisome proliferator‐activated receptor‐α (PPARα), in adipose tissue. However, in liver, the effects of palmitoleic acid on glucose metabolism and the role of PPARα remain unknown. Objective: To investigate whether palmitoleic acid improved the hepatic insulin sensitivity of obese mice. Methods: C57BL6 and PPARα knockout (KO) mice were fed for 12 weeks with a standard diet (SD) or high‐fat diet (HF), and in the last 2 weeks were treated with oleic or palmitoleic acid. Results: Palmitoleic acid promoted a faster uptake of glucose in the body, associated with higher insulin concentration; however, even when stimulated with insulin, palmitoleic acid did not modulate the insulin pathway (AKT, IRS). Palmitoleic acid increased the phosphorylation of AMPK, upregulated glucokinase and downregulated SREBP‐1. Regarding AMPK downstream, palmitoleic acid increased the production of FGF‐21 and stimulated the expression of PPARα. Palmitoleic acid treatment did not increase AMPK phosphorylation, modulate glucokinase or increase FGF‐21 in liver of PPARα KO mice. Conclusions: In mice fed with a high‐fat diet, palmitoleic acid supplementation stimulated the uptake of glucose in liver through activation of AMPK and FGF‐21, dependent on PPARα. J. Cell. Physiol. 232: 2168–2177, 2017. © 2016 Wiley Periodicals, Inc.
The structure and transparency of the cornea

The cornea, belonging to the dioptric system of the eye and being part of its structural coat, must be both transparent and tough. Like other tissues of great tensile strength, the skin and sinews, it has a fibrous structure built up of collagen. The collagen fibres of the cornea are disposed in a layer, the substantia propria or stroma, which constitutes the greater part of its thickness. Unlike these other collagenous tissues the stroma is normally optically clear, but it tends to swell when in contact with fluid and becomes cloudy on swelling. This tendency is opposed by two cellular layers which cover the corneal surfaces, for if either of these layers is destroyed or severely damaged the stroma lying under the affected area will swell. Mechanical distortion of the cornea or compression of the eye-ball can also cloud the stroma; it clears instantly when the strain is removed. The explanation of the transparency of the stroma can have a satisfactory foundation only on a knowledge of its optical structure, that is, the geometric form, dimensions and refractive indices of its components. The first part of this paper is concerned with establishing this structure. In the second part the transmission of light across it, and the physical basis of its transparency are considered, and in the third the disturbance to the transparency caused by swelling and mechanical strain. The treatment of the problem of transparency and its solution, as given in this paper, have been the subject of a brief preliminary report (Maurice, 1954).
State Operator Correspondence and Entanglement in AdS2/CFT1

Since Euclidean global AdS2 space represented as a strip has two boundaries, the state-operator correspondence in the dual CFT1 reduces to the standard map from the operators acting on a single copy of the Hilbert space to states in the tensor product of two copies of the Hilbert space. Using this picture we argue that the corresponding states in the dual string theory living on AdS2 × K are described by the twisted version of the Hartle–Hawking states, the twists being generated by a large unitary group of symmetries that this string theory must possess. This formalism makes natural the dual interpretation of the black hole entropy—as the logarithm of the degeneracy of ground states of the quantum mechanics describing the low energy dynamics of the black hole, and also as an entanglement entropy between the two copies of the same quantum theory living on the two boundaries of global AdS2 separated by the event horizon.
Spanning sets for automorphic forms and dynamics of the frame flow on complex hyperbolic spaces

Let G be a semisimple Lie group with no compact factors, K a maximal compact subgroup of G, and \Gamma a lattice in G. We study automorphic forms for \Gamma if G is of real rank one with some additional assumptions, using a dynamical approach based on properties of the homogeneous flow on \Gamma\backslash G and a Livshitz type theorem we prove for such a flow. In the Hermitian case G=SU(n,1) we construct relative Poincaré series associated to closed geodesics on \Gamma\backslash G/K for one-dimensional representations of K, and prove that they span the corresponding spaces of holomorphic cusp forms.
Kinetics of serum cytokines after primary or repeat vaccination with the smallpox vaccine.

BACKGROUND The smallpox vaccine is associated with more serious adverse events than any other live attenuated vaccine in use today. Although studies have examined serum cytokine levels in primary vaccine recipients at 1 and 3-5 weeks after vaccination with the smallpox vaccine, serial measurements have not been performed, and studies in revaccinated subjects have not been conducted. METHODS We analyzed cytokine responses in both primary vaccine recipients and revaccinated subjects every other day for 2 weeks after vaccination. RESULTS Primary vaccine recipients had maximal levels of granulocyte-colony-stimulating factor on days 6-7 after vaccination; peak levels of tumor necrosis factor (TNF)-alpha, soluble TNF receptor 1, interferon (IFN)-gamma, IFN-inducible protein-10 (IP-10), interleukin (IL)-6, and tissue inhibitor of metalloproteinases-1 on days 8-9 after vaccination; peak levels of soluble TNF receptor 2 and monokine induced by IFN-gamma (MIG) on days 10-11 after vaccination; and peak levels of granulocyte-macrophage-colony-stimulating factor on days 12-13 after vaccination. Primary vaccine recipients were significantly more likely to have higher peak levels of IFN-gamma, IP-10, and MIG after vaccination than were revaccinated subjects. Primary vaccine recipients were significantly more likely to have fatigue, lymphadenopathy, and headache, as well as a longer duration of these symptoms and more hours missed from work, compared with revaccinated subjects. CONCLUSIONS The increased frequency and duration of symptoms observed in primary vaccine recipients, compared with revaccinated subjects, paralleled the increases in serum cytokine levels in these individuals. TRIAL REGISTRATION Clinicaltrials.gov identifier NCT00325975.
An approach to identify user interest by reranking personalize web

The existence of abundance information, in combination with the heterogeneous and dynamic nature of the web, makes web exploration a complex process for the average end user. Lower ability of user to precisely express the need and ambiguous queries are the challenging obstacle in improving search results. Retrieved results are sometimes not of user relevance due to keyword based search, so to fill the gap between retrieved result and user interest we need to personalize the results. For example, a biologist and a programmer may use the same query "mouse" with different search context, but the search systems would return same results. In this paper we proposed an architecture that attempts to identify user search context by analyzing and mapping semantic data using semantic similarity to predict the query topic.
Developing effective customer-supplier relationships: more than one way to skin a cat.

The paper uses data from a questionnaire survey of UK firms to examine the ways in which benefits and costs are divided in buyer‐supplier relationships. These results are analysed in the light of Burnes and New′s framework for considering supply chain improvement. The results indicate that some caution is required in the applicability of the notion of “win‐win” in buyer‐supplier collaborations. Conclusions are drawn for theory and practice.