Miracle-dz/UniFAR-FTUs huggingface dataset:
Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge community

Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge community David L. Mobley 1 , John D. Chodera 2 and Michael K. Gilson 3 of Pharmaceutical Sciences and Chemistry, University of California, Irvine 2 Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center 3 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 1 Departments Abstract: The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind prediction challenges provide unbiased, prospective tests of computational methods, serving as a crowdsourcing mechanism to drive innovation. These challenges solicit submissions from the computational community to predict properties of interest, such as solvation, partition, or binding of drug-like molecules. These challenges provided substantial benefit to the community, and have led to roughly 100 publications, many of which are broadly cited (see attached bibliography). We are currently seeking funding from the NIH and surveyed the community concerning experiences with SAMPL and how our future plans for SAMPL can best align with the community’s interests and needs. This document summarizes the results of this survey and describes our findings. On the whole, the community enthusiastically supports our plans for the future of SAMPL, and provided modest suggestions to further strengthen our plans. For up-to-date info please see the SAMPL website. Survey methods and results Here, we reproduce the results of the survey in full except for anonymizing respondents. Questions 1 and 2 dealt with identifying information (name and e-mail) and are thus bypassed here. There were 44 respondents, though not all respondents answered all questions. The survey was conducted via Google Forms from April 18 to June 19. The survey was advertised via Twitter and the Mobley Lab website, and e-mailed to to past participants.
Empirical Characterization of Mobility of Multi-Device Internet Users

Understanding the mobility of humans and their devices is a fundamental problem in mobile computing. While there has been much work on empirical analysis of human mobility using mobile device data, prior work has largely assumed devices to be independent and has not considered the implications of modern Internet users owning multiple mobile devices that exhibit correlated mobility patterns. Also, prior work has analyzed mobility at the spatial scale of the underlying mobile dataset and has not analyzed mobility characteristics at different spatial scales and its implications on system design. In this paper, we empirically analyze the mobility of modern Internet users owning multiple devices at multiple spatial scales using a large campus WiFi dataset. First, our results show that mobility of multiple devices belonging to a user needs to be analyzed and modeled as a group, rather than independently, and that there are substantial differences in the correlations exhibited by device trajectories across users that also need to be considered. Second, our analysis shows that the mobility of users shows different characteristics at different spatial scales such as within and across buildings. Third, we demonstrate the implications of these results by presenting generative models that highlight the importance of considering the spatial scale of mobility as well as multi-device mobility. More broadly, our empirical results point to the need for new modeling research to fully capture the nuances of mobility of modern multi-device users.
Psychometric Properties of the MacArthur Community Violence Screening Instrument

Abstract This study examined the psychometric properties of the MacArthur Community Violence Screening Instrument (MCVSI) in a heterogeneous and integrated sample of adults with mental illness (n = 4,480), including its factor structure, model fit, and psychometric properties as a function of patient sex, race, and primary diagnosis. Factor structure results indicate a unidimensional construct. Item-level analyses revealed that the MCVSI’s difficulty, including the easiest and most difficult items to endorse, sometimes differed across sex, race, and primary diagnosis. However, differential item functioning was minimal across these patient characteristics, with only those without a primary diagnosis of schizophrenia indicating an increased likelihood of having “hit anyone with a fist, object or beaten anyone” compared to those with a primary diagnosis of schizophrenia. Overall, these findings support using the MCVSI as a measure of violence in studies of U.S. adults with mental illness. They also highlight the importance of using more methodologically rigorous approaches to measuring violence, including the ongoing study of the MCVSI across samples and settings.
What gamification design do users want in a self-management application for chronic diseases? - The case of Cystic Fibrosis

The aim of this thesis is to improve self-management of chronic disease by utilizing gamification in an mHealth app to increase users’ motivation. This thesis focuses on Cystic Fibrosis (CF), a rare genetic disorder found in about 70.000 people worldwide. People diagnosed with CF must follow strict treatment regimens in order to maintain health and well being, posing a challenge for patient adherence. The thesis departs from earlier research done by MyCyFAPP, a project creating software solutions for self-management of CF. In this study we have identified patients’ needs and challenges and used them with principles from existing gamification design methods to create an ideation workshop consisting of semistructured interviews and co-design activities. The workshop was tested, revised and finally conducted with two people diagnosed with CF, resulting in 4 hours of captured audio and 41 gamification design ideas. The results were analyzed and used to create a list of gamification design ideas wanted by participants, and gamification design examples for improving MyCyFAPP’s smartphone app. Our findings confirm that the participants would like gamification in an application for CF selfmanagement to attempt to increase their motivation. Specifically, participants would like social interaction to communicate with each other. They would also like the application to empower them to create, and fulfill treatment goals by increasing their knowledge and competence. Finally the findings show that the participants would like to progress by feeling and tracking progression, and understanding how to improve. In addition to a complete list of gamification design ideas, this thesis also provides gamification design examples inspired by the findings, and a complete user-centered approach on how to plan and conduct a co-design workshop for gamification solutions in an app for self-management of Cystic Fibrosis.
vRNA-vRNA interactions in influenza A virus HA vRNA packaging

The genome of the influenza A virus is composed of eight single-stranded negative-sense RNA segments (vRNAs). The eight different vRNAs are selectively packaged into progeny virions. This process likely involves specific interactions among vRNAs via segment-specific packaging signals located in the 3’ and 5’ terminal coding regions of vRNAs. To identify vRNA(s) that interact with hemagglutinin (HA) vRNA during genome packaging, we generated a mutant virus, HA 5m2, which possessed five silent mutations in the 5’ packaging signal region of HA vRNA. The HA 5m2 virus had a specific defect in HA vRNA incorporation, which reduced the viral replication efficiency. After serial passaging in cells, the virus acquired additional mutations in the 5’ terminal packaging signal regions of both HA and PB2 vRNAs. These mutations contributed to recovery of viral growth and packaging efficiency of HA vRNA. A direct RNA-RNA interaction between the 5’ ends of HA and PB2 vRNAs was confirmed in vitro. Our results indicate that direct interactions of HA vRNA with PB2 vRNA via their packaging signal regions are important for selective genome packaging and enhance our knowledge on the emergence of pandemic influenza viruses through genetic reassortment.
Influence of Flexibility of the Interconnects on the Dynamic Bending Reliability of Flexible Hybrid Electronics

The growing interest towards thinner and conformable electronic systems has attracted significant attention towards flexible hybrid electronics (FHE). Thin chip-foil packages fabricated by integrating ultra-thin monocrystalline silicon integrated circuits (ICs) on/in flexible foils have the potential to deliver high performance electrical functionalities at very low power requirements while being mechanically flexible. However, only very limited information is available regarding the fatigue or dynamic bending reliability of such chip-foil packages. This paper reports a series of experiments where the influence of the type of metal constituting the interconnects on the foil substrates on their dynamic bending reliability has been analyzed. The test results show that chip-foil packages with interconnects fabricated from a highly flexible metal like gold endure the repeated bending tests better than chip-foil packages with stiffer interconnects fabricated from copper or aluminum. We conclude that further analysis work in this field will lead to new technical concepts and designs for reliable foil based electronics.
Loop-mediated isothermal ampli ﬁ cation (LAMP) – review and classi ﬁ cation of methods for sequence-speci ﬁ c detection

In the course of the last 20 years, isothermal nucleic acid ampli ﬁ cation tests have emerged as an important diagnostic tool, not only for clinical applications, but also for food quality control and environmental monitoring. Loop-mediated isothermal ampli ﬁ cation (LAMP) is well known for its robust and highly sensitive and speci ﬁ c ampli ﬁ cation of target DNA, which is achieved by utilizing up to six primers. Moreover, LAMP excels through its isothermal and energy e ﬃ cient ampli ﬁ cation requirements, rendering it a prime candidate for low-cost diagnostics and analysis at the point of need. Recently, methods for sequence-speci ﬁ c detection have gained more importance because, unlike sequence-independent detection methods, they are highly speci ﬁ c towards the target DNA. In the last 13 years, a variety of sequence-speci ﬁ c methods have emerged, based on a very diverse range of sensing techniques, including optical, magnetic, piezoelectric, electrochemical and magnetoresistive sensing. To give structure to the diverse multitude of sequence-speci ﬁ c methods, we created a systematic classi ﬁ cation and provide a critical comparative evaluation according to a catalogue of criteria (analytical performance, multiplexing, quanti ﬁ cation and instrumental requirements). Fluorescence-based detection, making up half of the methods, can be processed on open platforms and satis ﬁ es all the criteria listed before. Instrumental requirements are discussed in terms of complexity, portability and ﬂ uidic cartridges. In addition, the technological readiness level and the kind of platform (open versus method-tailored) are evaluated, the latter playing an important role in the miniaturization and automation of operational process steps. We also observe an increase in the use of smartphone-integrated sensors to improve LAMP-based point-of-need testing. In summary, recent developments in methods for the sequence-speci ﬁ c detection of LAMP demonstrate high potential for many future applications.
Orienting and locating ocean-bottom seismometers from ship noise analysis

Breakthroughs in understanding the structure and dynamics of our planet will strongly depend upon instrumenting deep oceans. Progress has been made these last decades in ocean-bottom seismic observations, but ocean-bottom seismometer (OBS) temporary deployments are still challenging and face setup limitations. Launched from oceanographic vessels, OBSs fall freely and may slightly drift laterally, dragged by currents. Therefore, their actual orientation and location on the landing sites are hard to assess precisely. Numerous techniques have been developed to retrieve this key information, but most of them are costly, time-consuming or inaccurate. In this work, we show how ship noise can be used as an acoustic source of opportunity to retrieve both the orientation and the location of OBSs on the ocean floor. To retrieve the OBS orientation, we developed a first method based on a combination of seismic and pressure data through the use of the acoustic intensity. This latter can be used to quantify the OBS orientation from the ship noise direction of arrival (DOA), which can then be compared with known ship trajectories obtained from the automatic identification system (AIS). To accurately relocate OBSs, we also developed a second method based on the hydrophone data which computes distances of acoustical sources by measuring time differences of arrival (TDOA) between direct and reverberated phases. The OBS location is then retrieved by fitting measured ship distances with known ship trajectories. In this study, a full network of OBSs deployed in the SW Indian Ocean was reoriented and a test station was relocated. We demonstrate that our new methods may quantify the OBS orientation with an accuracy of about one degree, and its location with an accuracy of a few tens of metres, depending on the number of ships used in the analysis.
Preliminary Notes on the Term and Institution of al-Shākiriyya in Early Islam (ca. 14–218 H/635–36–833 CE) Mainly According to the Arabic Sources

The aim of this paper is to study the nature of the term and institution of al-Sh ā kiriyya by re-examining the Arabic sources pertaining to the Umaw ī and early ʿ Abb ā s ī caliphate. It is difficult to discern the character of the Sh ā kiriyya in the service of the Arab commanders in Central Asia from the Arabic sources. They provide no information on ethnic composition, mobilization, military training or potential ties between a commander/master and his Sh ā kir . This applies mainly to the Umaw ī period, but also to the first ʿ Abb ā s ī period up to al-Ma ʾ m ū n ’ s rule (813 – 833). It is also impossible to determine from them the possible connections between the ancient Central Asian military institutions and military institutions in the Islamic world. From evidence about the Sh ā kiriyya in the Arabic sources we can usually discern a distinct military character, though it is noteworthy that in some cases the term Sh ā kir ī can be translated as meaning a loyal adherent, or even a servant.While relatively extensive, the evidence at hand from the Umaw ī and the early ʿ Abb ā s ī periods is too limited to fully demonstrate that a) the Sh ā kiriyya units denote Turks and b) that these allegedly Turkish units performed their service for the ʿ Abb ā s ī caliphs according to concepts and practices derived from the Central Asian steppe. al-Mas ū d s Mur ū j al-Dhahab ], but history here is envisaged from a more phil-osophical and certainly from a more critical point of view. The author displays a good knowledge of ancient and alien religions,whose cultural value he stresses without however ceasing to place Islam above them. He follows the usual order. Beginning with the creation of the world, he devotes the first three volumes (half of the whole work) to ancient history and to philosophical, theological, geographical, etc. considerations and does not reach a consideration of Islam until the fourth volume (cf. the parallel lay-out of al-Mas ʿ ū d ī ’ s work, in which these earlier topics occupy two out of five), finally reserving a restricted place for the Umayyads and ʿ Abb ā s ī ds … a disdain may possibly arise precisely from the originality and free thought of a writer who seems to have maintained a certain independence and not to have been an adherent of any religious movement of age when lived. ³
Stroke Survivor and Family Caregiver Reports of Caregiver Engagement in Stroke Care.

PURPOSE The aim of the study was to identify areas of caregiver engagement in stroke care as viewed by stroke survivors and family caregivers. DESIGN Interviews with stroke survivor/caregiver dyads (N = 71) from a population-based study of incident stroke. METHODS We interviewed stroke survivors and caregivers about caregiver involvement at multiple stages of stroke care. We assessed similarities and differences between stroke survivor and caregiver reports and analyzed responses to open-ended questions. FINDINGS Stroke survivor and caregiver reports of engagement were highly correlated (r = .89), although caregivers reported higher involvement. Open-ended comments suggested that, in about 25% of cases, stroke survivors and caregivers agreed that caregiver engagement led to major improvements in stroke survivor care, most commonly during onset of symptoms. CONCLUSIONS Stroke survivors and caregivers report significant and impactful caregiver engagement throughout the course of stroke. CLINICAL RELEVANCE Clinicians may enhance stroke care by recognizing and facilitating caregiver efforts across all phases of stroke care.
Effects of Control-Display Mapping and Spatially Dependent Gain on Supported Free-Hand Gesture Pointing Performance

While gesture controls will be important as future computing input modalities, they are limited by reduced performance and increase ergonomic risk. Performance of pointing in free-hand gestural controls is affected by control-display (CD) parameters such as gain and mapping, but specific CD function parameters that yield optimal performance are unclear. This paper describes an experiment that examines the effect of altering CD gain in different movement directions (‘spatially dependent gain’, SDG) for different CD mappings on their performance in armrest-supported pointing tasks. Thirteen participants were given a series of circular Fitts’ tasks with different fixed CD gain and mapping settings. The SDG was used to warp the Fitts’ circle in the participants’ physical motor-space in order to take advantage of inherent motor performance differences. Additionally, the placement of the movement controller was also studied. The results show that mapping is the most significant factor; vertical mapping produced throughput results that were approximately 0.5 bits/s greater on average than the other mappings. Vertical mapping is also where CD gain shows the most effect. Lower gain settings produce results that are 0.14 bits/s faster than higher gain when the user is in vertical mapping. No significant differences were found in pointing performance between SDG conditions. These preliminary results suggest that participants adapt easily to motor-space warping and that further study of non-fixed gain functions (e.g. pointer acceleration functions) is necessary in order to maximize free-hand performance.
Coronary angiographic findings among diabetic and non-diabetic patients

objectives: Atherosclerotic coronary artery disease (CAD) is a major cause of death all over the world. Among patients with CAD there are many of them having diabetes mellitus which is regarded as a major additive risk factor. Diabetic patients who developed CAD carry high morbidity and mortality rates. The objective of this study was to analyze the coronary angiographic outcome of patients with type two diabetes mellitus suspected to have coronary artery disease and comparing these results with non-diabetic patients. Methods: Patients referred to Mosul Cardiac Catheterization Unit of Ibn-Sena Teaching Hospital for coronary angiography were serially included until obtaining a total of 75 diabetic and 75 non-diabetic patients with predicted coronary artery disease and with different ischemic heart disease risk factors including obesity, smoking, hypertension and dyslipidemia. All of them underwent coronary angiography. Result: Diabetic patients showed more significant stenotic lesions. Moreover the lesions in the coronary artery were more diffuse with higher incidence of multivessel involvement in comparison to non-diabetic patients. Also diabetic patients show increasing incidence of the left main stem artery involvement which carry very high mortality rate. Conclusion: Diabetes mellitus is an independent risk factor for coronary artery disease associated with more advanced, serious and extensive obstructive atherosclerotic lesions in the coronary arteries.
Effect of different slaughtering methods on metabolites of broiler chickens using Ultra High-Performance Liquid Chromatography-Time of Flight-Mass Spectrometry (UHPLC-TOF-MS)

Ali, N.S.M. , Zabidi, A.R. , Manap, M.N. A. , Zahari, S.M.S.N.S. and Yahaya, N. Department of Food Biotechnology, Faculty of Science and Technology, Universiti Sains Islam Malaysia, 71800, Nilai, Negeri Sembilan, Malaysia Department of Industrial Chemical Technology, Faculty of Science and Technology, Universiti Sains Islam Malaysia, 71800, Nilai, Negeri Sembilan, Malaysia International Fatwa and Halal (iFFAH) Center, Universiti Sains Islam Malaysia, 71800, Nilai, Negeri Sembilan, Malaysia
Defining major trauma: a pre-hospital perspective using focus groups

Background: Pre-hospital trauma is complex and challenging, with limited clinical exposure for clinicians. In addition, there is no standardised definition for major trauma, and retrospective scores commonly quantify injury severity, such as the injury severity score. This qualitative study aimed to explore the pre-hospital perspectives of major trauma and how pre-hospital trauma care providers define major trauma. Method: Three focus groups of 40–60 minutes’ duration were conducted with paramedics, ambulance technicians, police, firefighters and emergency dispatchers. Digital recordings were transcribed verbatim, coded and reviewed to identify emerging themes. Constant comparison was undertaken throughout and codes were identified for qualitative thematic analysis. Results: Three overarching themes emerged: clinician factors, patient factors and situational factors. Clinician factors highlighted issues of experience and exposure (or lack of) to major trauma and its relationship to clinical concern, communication issues and the complex nature of pre-hospital trauma. Patient factors identified deranged physiology, actual injuries, life changing trauma, potential need for surgical intervention and rehabilitation as defining major trauma. These variables are often complicated by the extremities of age as well as previous medical history and medications. The situational factors identified that every traumatic encounter is unique, requiring bespoke management where high and low energy mechanisms of injury should be considered. Conclusion: Based on the analysis of the focus groups, a working pre-hospital definition is: Any injury (or injuries) that have the potential to be life-threatening or life-changing, including those sustained from low energy mechanisms in people rendered vulnerable by extremes of age, comorbidities or frailty, resulting in significant physiological compromise (haemodynamic instability, reduced consciousness, respiratory compromise) and/or significant anatomical abnormality that may require immediate intervention.