Miracle-dz/UniFAR-FTUs huggingface dataset:
The N-terminal Membrane Occupation and Recognition Nexus Domain of Arabidopsis Phosphatidylinositol Phosphate Kinase 1 Regulates Enzyme Activity*

The type I B family of phosphatidylinositol phosphate kinases (PIPKs) contain a characteristic region of Membrane Occupation and Recognition Nexus (MORN) motifs at the N terminus. These MORN motifs are not found in PIPKs from other eukaryotes. To understand the impact of the additional N-terminal domain on protein function and subcellular distribution, we expressed truncated and full-length versions of AtPIPK1, one member of this family of PIPKs, in Escherichia coli and in tobacco cells grown in suspension culture. Deletion of the N-terminal MORN domain (amino acids 1–251) of AtPIPK1 increased the specific activity of the remaining C-terminal peptide (ΔMORN) >4-fold and eliminated activation by phosphatidic acid (PtdOH). PtdOH activation could also be eliminated by mutating Pro396 to Ala (P396A) in the predicted linker region between the MORN and the kinase homology domains. AtPIPK1 is product-activated and the MORN domain binds PtdIns(4,5)P2. Adding back the MORN peptide to ΔMORN or to the PtdOH-activated full-length protein increased activity ∼2-fold. Furthermore, expressing the MORN domain in vivo increased the plasma membrane PtdInsP kinase activity. When cells were exposed to hyperosmotic stress, the MORN peptide redistributed from the plasma membrane to a lower phase or endomembrane fraction. In addition, endogenous PtdInsP kinase activity increased in the endomembrane fraction of hyperosmotically stressed cells. We conclude that the MORN peptide can regulate both the function and distribution of the enzyme in a manner that is sensitive to the lipid environment.
An expanded role for semaphorin 4D in platelets includes contact‐dependent amplification of Clec‐2 signaling

Semaphorins are cell surface proteins sharing an extracellular Sema motif that binds to plexin family receptors, among others [1]. We have shown previously that Sema4D is expressed by platelets, serving as a contact-dependent amplifier of platelet activation by promoting activation of the tyrosine kinase, Syk, downstream of the collagen receptor, GP VI/FcRγ [2–4]. Deletion of Sema4D impairs thrombus growth in mice by reducing the number of fully-activated, stably-adherent platelets in the region closest to the vessel wall [5]. Sema4D(−/−) platelets have diminished responses to collagen, but normal responses to thrombin, TxA2 and ADP [2, 4]. Collagen-induced Syk activation and the subsequent activation of phospholipase Cγ2 are most robust when Sema4D is present and platelets are allowed to form stable contacts [4]. These observations have helped to define the role of platelet Sema4D. In the setting of vascular injury, Syk is activated by binding to a phosphorylated immunoreceptor tyrosine-based activation motif (ITAM) in FcRγ. However, while our previous studies show that Sema4D does not amplify G protein-dependent signaling, left unsettled was whether signal amplification is specific for GPVI or applies to other ITAM receptors as well. Here we have addressed that issue. Human platelets express two other ITAM-containing receptors, Clec-2 and FcR-IIA. Mouse platelets express Clec-2 [6]. Unlike GPVI/FcRγ and FcR-IIA, Clec-2 contains only half of an ITAM motif or “hemi-ITAM” (YXXL). Signaling occurs when two molecules of phosphorylated Clec-2 engage a single molecule of Syk [6, 7]. The known Clec-2 ligands are the snake venom toxin, rhodocytin [6] and podoplanin. Podoplanin/Clec-2 interactions play an essential role in separating the lymphatic and vascular systems during embryonic development [8–10].
Tandem learning: a learning framework for document categorization

Supervised machine learning techniques rely on the availability of ample training data in the form of labeled instances. However, in text, users can have a strong intuition about the relevance of features, that is, words that are indicative of a topic. In this work we show that user prior knowledge on features is useful for text classification, a domain with many irrelevant and redundant features. The benefit of feature selection is more pronounced when the objective is to learn a classifier with as few training examples as possible. We will demonstrate the role of feature feedback in training a classifier to suitable performance quickly. We find that aggressive feature feedback is necessary to focus the classifier during the early stages of active learning by mitigating the Hughes phenomenon. We will describe an algorithm for tandem learning that begins with a couple of labeled instances, and then at each iteration recommends features and instances for a user to label. The algorithm contains methods to incorporate feature feedback into Support Vector Machines. We design an oracle to estimate an upper bound on tandem learning performance. Tandem learning using an oracle results in much better performance than learning on only features or only instances. We find that humans can emulate the oracle to an extent that results in performance (accuracy) comparable to that of the oracle. Our unique experimental design helps factor out system error from human error, leading to a better understanding of when and why interactive feature selection works from a user perspective. We also design a set of difficulty measures that capture the inherent instance and feature complexity of a problem. We verify the robustness of our measures by showing how instance and feature complexity are highly correlated. Our complexity measures serve as a tool to understand when tandem learning is beneficial for text classification.
Lower limb joint kinetics during moderately sloped running.

CONTEXT Knowledge of the kinetic changes that occur during sloped running is important in understanding the adaptive gait-control mechanisms at work and can provide additional information about the poorly understood relationship between injury and changes in kinetic forces in the lower extremity. A study of these potential kinetic changes merits consideration, because training and return-to-activity programs are potentially modifiable factors for tissue stress and injury risk. OBJECTIVE To contribute further to the understanding of hill running by quantifying the 3-dimensional alterations in joint kinetics during moderately sloped decline, level, and incline running in a group of healthy runners. DESIGN Crossover study. SETTING Three-dimensional motion analysis laboratory. PATIENTS OR OTHER PARTICIPANTS Nineteen healthy young runners/joggers (age = 25.3 +/- 2.5 years). INTERVENTION(S) Participants ran at 3.13 m/s on a treadmill under the following 3 different running-surface slope conditions: 4 degrees decline, level, and 4 degrees incline. MAIN OUTCOME MEASURE(S) Lower extremity joint moments and powers and the 3 components of the ground reaction force. RESULTS Moderate changes in running-surface slope had a minimal effect on ankle, knee, and hip joint kinetics when velocity was held constant. Only changes in knee power absorption (increased with decline-slope running) and hip power (increased generation on incline-slope running and increased absorption on decline-slope running in early stance) were noted. We observed an increase only in the impact peak of the vertical ground reaction force component during decline-slope running, whereas the nonvertical components displayed no differences. CONCLUSIONS Running style modifications associated with running on moderate slopes did not manifest as changes in 3-dimensional joint moments or in the active peaks of the ground reaction force. Our data indicate that running on level and moderately inclined slopes appears to be a safe component of training regimens and return-to-run protocols after injury.
A personalized recommender system for digital libraries

This paper presents the evaluation of a Recommender System for scientific articles in digital libraries. This system is geared towards the Computer Science scientific community. Technologically speaking, the proposed system was developed under the Semantic Web perspective since it explores its emergent technologies such as the use of standard metadata for document description (i.e., Dublin Core), XML for user's profile description (i.e., Lattes Curriculum Vitae), and Web services and data providers (OAI) involved on the recommendations' generation process. The focus of this paper is the presentation and discussion of the extended experimental evaluation results obtained with a Web prototype.
Unveiling the Expression Characteristics of IspC, a Cell Wall-Associated Peptidoglycan Hydrolase in Listeria monocytogenes, during Growth under Stress Conditions

ABSTRACT Listeria monocytogenes serotype 4b is a food-borne pathogen of public health concern, since it accounts for approximately 40% of human listeriosis cases. We have recently identified IspC, a surface-localized peptidoglycan hydrolase, as the antigen recognized by a number of monoclonal antibodies (MAbs) produced against a serotype 4b strain for diagnostic applications. To determine whether IspC, which is well conserved among various serotype 4b strains, is a useful diagnostic marker in antibody-based methods, we assessed the expression of IspC in L. monocytogenes cultured under normal and stress conditions. A functional promoter directing the transcription of the ispC gene was identified upstream of the ispC open reading frame by constructing a promoterless lacZ gene fusion with the putative ispC promoter region and by 5′ rapid amplification of cDNA ends analysis. Using both the lacZ reporter gene system and immunofluorescent staining with an IspC-specific MAb, we provide evidence that IspC is expressed on the cell surface in all growth conditions tested (temperature, osmotic stress, pH, ethanol, oxidative stress, anaerobic conditions, carbon source, and type of growth media) that allow for cellular division, although the level of ispC gene expression varies. These results demonstrated the usefulness of IspC as an excellent diagnostic marker for the serotype 4b strains and imply that IspC, in conjunction with specific MAbs, can be targeted for detection and isolation of L. monocytogenes serotype 4b strains directly from food, environmental, and clinical samples with minimal or no need for culture enrichment.
Effects of adhesive drapes on contamination of operation wounds.

Abstract Counts of viable bacteria were made on fluid used for irrigation of 10 operation wounds (nail-plating of neck of femur) for which the skin had been covered with adhesive drape (' Steridrape '), and in 12 similar operation wounds in which adhesive drapes had not been used. There was no significant difference in the mean numbers of bacteria found in the two series of wounds. Counts of samples taken at the beginning of operations were slightly but not significantly higher than those taken at the end of operations. Small numbers of Staphylococcus aureus were found in 4 of the 22 wounds. There was no evidence of an increase in bacteria on normal skin covered by steridrape for up to four hours. It is concluded that adhesive drapes probably give no protection against bacterial contamination of operation wounds.
Surgical Challenges in Transplantation: The Fourth Annual American Society of Transplant Surgeons' State‐of‐the‐Art Winter Symposium

aDepartment of Surgery, Division of Transplantation, University of California San Francisco bDepartment of Surgery, University of Minnesota cDepartment of Surgery, Lahey Clinic Medical Center, Tufts Medical School dDepartment of Surgery, Georgetown University eDepartment of Surgery, Division of Transplantation, University of Tennessee ∗Corresponding author: Sandy Feng, M.D., Ph.D., fengs@surgery.ucsf. edu
Mycotic Aneurysm of the Descending Thoracic Aorta Caused by Haemophilus Influenzae

Abstract A 59‐year‐old man presented with a three‐month history of back pain, and enhanced computed tomography demonstrated an acutely expanding aneurysm of the descending thoracic aorta with slight erosion of the corresponding vertebrae. Because of suspected infectious or inflammatory etiology, he was managed with a combination of emergency aortic repair using prosthetic graft with omental flap and antibiotic chemotherapy. Haemophilus influenzae was identified from perioperative specimens and the postoperative course was uneventful. (J Card Surg 2010;25:218‐220)
Correction of Tailor's Bunion with the Boesch Technique: A Retrospective Study

Background The Boesch technique1,2 is a minimally-invasive and time-saving subcutaneous subcapital metatarsal osteotomy. Since 1984, we have been using this osteotomy technique for patients with a symptomatic tailor's bunion in whom conservative treatment has failed. This distal osteotomy is stabilized by a combination of a Kirschner wire and a special dressing. The results of this technique in patients with symptomatic tailor's bunion were reviewed. Methods Between March, 1998, and June, 2002, surgery was done in 77 feet of 65 patients with a mean age of 64.6 years. The mean followup was 56.6 (range 14 to 79) months. The 100-point American Orthopaedic foot and Ankle Society (AOFAS) Lesser Metatarsophalangeal-Interphalangeal Scale was used for scoring. Results 86.4% of 57 patients (66 feet) were free of pain at final followup. The mean 4–5 intermetatarsal angle was 12 degrees before and 8 degrees after surgery. The mean lateral deviation of the fifth metatarsal was 5.7 degrees before and 5.1 degrees after surgery. The mean fifth metatarsophalangeal angle was 17.8 degrees before and 6.2 degrees after surgery. The mean preoperative 100-point AOFAS score was 59.1 (range 23 to 88) and the postoperative score, 95.2 (range 73 to 100). The overall results were excellent in 87.9%, (58 feet) good in 6.1% (4 feet), and satisfactory in 6.1%; none was poor. Conclusions The advantages of the subcutaneous subcapital Boesch technique are that it is time saving, it causes less bone and soft-tissue trauma, and it is performed under local anesthesia without a tourniquet. It is an effective operative option for symptomatic tailor's bunion; excellent and good clinical and radiographic results were found in 86.4% (57 patients, 66 feet) of the patients.
The Role of Socioeconomic Status in Medical School Admissions: Validation of a Socioeconomic Indicator for Use in Medical School Admissions

Purpose Socioeconomic status (SES) impacts educational opportunities and outcomes which explains, in part, why the majority of medical students come from the upper two quintiles of family income. A two-factor SES indicator based on parental education (E) and occupation (O) has recently been established by the Association of American Medical Colleges (AAMC). This study validates this two-factor indicator as applicable to the national pool of medical school applicants. Method The AAMC SES EO indicator classifies applicants into five ordered groups (EO-1 through EO-5) based on four aggregated categories of parental education and two aggregated categories of occupation. The EO indicator was applied to the 2012 American Medical College Application Service applicant pool. The authors examined the associations that the EO category had with six additional and independent indicators of socioeconomic (dis)advantage, as well as with demographic and educational characteristics and life experiences. Results The EO indicator could be applied to 89% of the 2012 applicants. The lower the EO category, the stronger the association with each of the six indicators of socioeconomic disadvantage. Other notable, but weaker, associations with the EO indicator were differences by age, race/ethnicity, performance on the Medical College Admission Test, community college attendance, and certain self-reported life experiences. Conclusions The EO indicator provides a simple, intuitive, widely applicable, and valid means for identifying applicants from socioeconomically disadvantaged backgrounds. This affords admissions committees an additional factor to consider during the holistic review of applicants in order to further diversify the medical school class.
Aspergillus calidoustus sp. nov., Causative Agent of Human Infections Previously Assigned to Aspergillus ustus

ABSTRACT Aspergillus ustus is a relatively rare human pathogen causing invasive infections in immunocompromised hosts. In this study isolates originating from clinical and other sources have been examined using molecular, morphological, and physiological approaches to clarify their species assignment. Phylogenetic analysis of partial β-tubulin, calmodulin, actin, and intergenic transcribed spacer sequences indicated that none of the clinical isolates recognized previously as A. ustus belongs to this species. All but two of these isolates formed a well-defined clade related to A. pseudodeflectus based on sequence analysis of protein-coding regions. Morphological and physiological examination of these isolates indicated that they are able to grow above 37°C, in contrast with A. ustus isolates, and give a positive Ehrlich reaction, in contrast with related species including A. granulosus, A. ustus, and A. pseudodeflectus. These isolates are proposed as a new species, A. calidoustus. Antifungal susceptibility testing showed that this species has decreased susceptibilities to several antifungal drugs. The triazoles are inactive in vitro, including the new azole posaconazole.
Sensor Data , Privacy , and Behavioral Tracking : Does Usage-Based Auto Insurance Benefit Drivers ?

Usage-Based Insurance (UBI) is a recent auto insurance innovation that enables insurance companies to collect individual-level driving data, provide feedback on driving performance, and offer individually targeted price discounts based on each consumer’s driving behavior. In this paper, using detailed information on insurance premiums, retention rates of customers, and individual driving behavior (from sensor data) for the UBI adopters, we examine and estimate the effect of the UBI policy on changing the customers’ driving behavior, which is a potential source of profit improvement for the insurance company beyond better selection among customers and higher retention rates. The key results of our analysis show that after UBI adoption, motorists improve their driving behavior, resulting in being safer drivers, providing a meaningful benefit for both the driver and the insurance company. We find that not all components of the UBI measure appear to change over time. In particular, we find that customers decrease their daily average hard brake frequency by an average of 21% after using UBI for six months, but we cannot find any significant effects on the mileage driven by customers after UBI adoption. We also find heterogeneous effects across different demographic groups. For example, younger drivers are more likely to adopt UBI and they also improve their UBI scores faster than older drivers after UBI adoption; and females show more improvement than males. We also find that economic incentives lead to higher adoption rates of UBI and greater improvements in driving behavior. Our results suggest that by sharing private consumer information with the insurance company, UBI is not only beneficial to the company, but also to consumers who become better drivers.
Using text mining to uncover students' technology-related problems in live video streaming

Because of their capacity to sift through large amounts of data, text mining and data mining are enabling higher education institutions to reveal valuable patterns in students' learning behaviours without having to resort to traditional survey methods. In an effort to uncover live video streaming (LVS) students' technology related-problems and to improve their learning experience, we applied text mining to data culled from LVS interactions. Our findings revealed low LVS student participation, which triggered us to initiate several actions to promote more active student participation. Our findings support previous studies regarding the effectiveness of data mining in transforming raw educational data into knowledge and decision-making tools. [ABSTRACT FROM AUTHOR]
A latent variable approach to measuring and explaining peace agreement strength

Abstract Much of the peace agreement durability literature assumes that stronger peace agreements are more likely to survive the trials of the post-conflict environment. This work does an excellent job identifying which provisions indicate that agreements are more likely to endure. However, there is no widely accepted way to directly measure the strength of agreements, and existing measures suffer from a lack of nuance or reliance on subjective weighting. We use a Bayesian item response theory model to develop a principled measure of the latent strength of peace agreements in civil conflicts from 1975 to 2005. We illustrate the measure's utility by exploring how various international factors such as sanctions and mediation contribute to the strength or weakness of agreements.
Survey of Sera from Encephalitis Patients for Balamuthia mandrillaris Antibody

More than 100 different infectious agents are known to cause encephalitis in humans, including viruses, bacteria, protozoa, and multicellular parasites. Balamuthiu mandrillaris is a free-living ameba that causes granulomatous amebic encephalitis (GAE) in both immunocompetent and immunocompromised individuals. Identified and isolated about a dozen years ago from a mandrill baboon [ 121, >SO cases have since been reported globally with 40 cases in the United States. As part of the California Encephalitis Project (CEP) a program to identify the etiologic agents involved in otherwise undiagnosed encephalitis cases we undertook screening of serum samples of encephalitis patients to look for evidence of Balan~utlzia CAE or exposure to Balunziirhiu as indicated by elevated antibody titers demonstrated by indirect iminunofluorescence (IIF).
Use of Fractional Factorial Designs in Antiviral Drug Studies

Experimental design and analysis is an effective and commonly used tool in scientific investigations and industrial applications. Many successful applications have been reported in engineering domains, such as chemical engineering, electrical engineering, and mechanical engineering. However, few cases have been reported in biological research, particularly in virology study. Antiviral drug combinations are increasingly used to reduce possible drug‐resistant viral mutant and reduce cytotoxicity. Drug combinations have often been reported to have higher efficacy and lower individual drug dosage. However, the combined antiviral drug effect is generally hard to assess. One important reason is due to the complex interactions between biological systems and drug molecules. We report a study using fractional factorial designs to investigate a biological system with Herpes simplex virus type 1 and five antiviral drugs. The experiment uses a novel composite design that consists of a 16‐run fractional factorial design and an 18‐run orthogonal array. The results indicate that two chemical drugs, Ribavirin and Acyclovir, are more effective than three Interferon drugs. Furthermore, significant interactions exist within the Interferon drug group and within the Ribavirin‐Acyclovir chemical drug group, but the interactions between the Interferon group and the chemical group are not significant. These observations have major implications in the understanding of antiviral drug mechanism towards better design of combinatorial antiviral drug therapy. Copyright © 2012 John Wiley & Sons, Ltd.