Miracle-dz/UniFAR-FTUs huggingface dataset:
DIRECT RADIO PROBING AND INTERPRETATION OF THE SUN'S PLASMA DENSITY PROFILE

The Sun's electron number density profile ne(r) is vital for solar physics but not well measured or understood within a few solar radii RS. Here, a new technique extracts ne(r) directly from coronal type III radio bursts for 40 ≤ f ≤ 180 MHz. Unexpectedly, wind-like regions with ne ∝ (r − RS)−2 are quite common below 2RS, and coronal type IIIs often have closely linear 1/f − t spectra. The profile ne ∝ (r − RS)−2 is consistent with the radio data and simulations and is interpreted in terms of conical flow from localized sources (e.g., UV funnels) close to the photosphere. It is consistent with solar wind acceleration occurring for 2 ≤ r/RS ≤ 10.
Darwin: A Genomics Co-processor Provides up to 15,000X Acceleration on Long Read Assembly

Genomics is transforming medicine and our understanding of life in fundamental ways. Genomics data, however, is far outpacing Moore»s Law. Third-generation sequencing technologies produce 100X longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. Over 1,300 CPU hours are required for reference-guided assembly of the human genome, and over 15,600 CPU hours are required for de novo assembly. This paper describes "Darwin" --- a co-processor for genomic sequence alignment that, without sacrificing sensitivity, provides up to $15,000X speedup over the state-of-the-art software for reference-guided assembly of third-generation reads. Darwin achieves this speedup through hardware/algorithm co-design, trading more easily accelerated alignment for less memory-intensive filtering, and by optimizing the memory system for filtering. Darwin combines a hardware-accelerated version of D-SOFT, a novel filtering algorithm, alignment at high speed, and with a hardware-accelerated version of GACT, a novel alignment algorithm. GACT generates near-optimal alignments of arbitrarily long genomic sequences using constant memory for the compute-intensive step. Darwin is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.
A Role for Programmed Cell Death in the Microbial Loop

The microbial loop is the conventional model by which nutrients and minerals are recycled in aquatic eco-systems. Biochemical pathways in different organisms become metabolically inter-connected such that nutrients are utilized, processed, released and re-utilized by others. The result is that unrelated individuals end up impacting each others' fitness directly through their metabolic activities. This study focused on the impact of programmed cell death (PCD) on a population's growth as well as its role in the exchange of carbon between two naturally co-occurring halophilic organisms. Flow cytometric, biochemical, 14C radioisotope tracing assays, and global transcriptomic analyses show that organic algal photosynthate released by Dunalliela salina cells undergoing PCD complements the nutritional needs of other non-PCD D. salina cells. This occurs in vitro in a carbon limited environment and enhances the growth of the population. In addition, a co-occurring heterotroph Halobacterium salinarum re-mineralizes the carbon providing elemental nutrients for the mixoheterotrophic chlorophyte. The significance of this is uncertain and the archaeon can also subsist entirely on the lysate of apoptotic algae. PCD is now well established in unicellular organisms; however its ecological relevance has been difficult to decipher. In this study we found that PCD in D. salina causes the release of organic nutrients such as glycerol, which can be used by others in the population as well as a co-occurring halophilic archaeon. H. salinarum also re-mineralizes the dissolved material promoting algal growth. PCD in D. salina was the mechanism for the flow of dissolved photosynthate between unrelated organisms. Ironically, programmed death plays a central role in an organism's own population growth and in the exchange of nutrients in the microbial loop.
An mHealth System for Monitoring Medication Adherence in Obstructive Respiratory Diseases Using Content Based Audio Classification

Asthma and chronic obstructive pulmonary disease are obstructive respiratory diseases that affect negatively the quality of life for patients and their families worldwide. Despite the significance of these diseases, their management has been considered suboptimal around the world, whereas the improper inhaler use has been underlined as one of the main causes. Toward this direction, this paper presents an integrated mHealth system that provides real-time personalized feedback to patients for assessing the proper medication use and educating them and helping them avoid common mistakes. The identification of proper inhaler use is based on conventional and data-driven feature extraction and classification methods employed for the identification of four events (inhaler actuation, inhalation, exhalation, and background noise). The proposed scheme reaches 98% classification accuracy significantly outperforming recent and relevant state-of-the-art approaches. Finally, intuitive feedback interfaces were implemented in the form of a virtual guidance agent integrated with the mobile application, which can help patients follow their action plan and assess their inhaler technique in a more engaging manner. Extensive simulation studies, carried out using 12 subjects, demonstrated the efficiency of the proposed approaches in both indoor and outdoor environments.
Effect of Family Caregiving on Depression in the First 3 Months After Spinal Cord Injury

Objective To investigate the effect of family caregiving on depression in the first 3 months after spinal cord injury (SCI). Methods A retrospective study was carried out on 76 patients diagnosed with an SCI from January 2013 to December 2016 at the Department of Physical Medicine and Rehabilitation of Kyungpook National University Hospital, Korea. Clinical characteristics including age, gender, level of injury, completeness of the injury, time since injury, caregiver information, etiology, and functional data were collected through a retrospective review of medical records. Depression was assessed using the Beck Depression Inventory (BDI). Patients with 14 or more points were classified as depressed and those with scores of 13 or less as non-depressed group. Results Of the 76 patients, 33 were in the depressed group with an average BDI of 21.27±6.17 and 43 patients included in the non-depressed group with an average BDI of 4.56±4.20. The BDI score of patients cared by unlicensed assistive personnel (UAP) was significantly higher than that of patients cared by their families (p=0.020). Univariate regression analysis showed that motor complete injury (p=0.027), UAP caregiving (p=0.022), and Ambulatory Motor Index (p=0.019) were associated with depression after SCI. Multivariate binary logistic regression analysis showed that motor completeness (p=0.002) and UAP caregiving (p=0.002) were independent risk factors. Conclusion Compared with UAP, family caregivers lowered the prevalence of depression in the first 3 months after SCI.
Study on the levels of uric acid and high-sensitivity C-reactive protein in ACS patients and their relationships with the extent of the coronary artery lesion.

OBJECTIVE We evaluated uric acid (UA) and high-sensitivity C-reactive protein (hs-CRP) levels in different clinical types of acute coronary syndromes (ACS) and in relationship with the severity of coronary artery lesions. Furthermore, we explored its clinical significance. PATIENTS AND METHODS From June 2013 to January 2015, we studied patients in their first onset of symptoms and hospitalization for coronary angiography. According to coronary angiography results, we divided patients into two groups: 93 patients with ACS and 30 patients with normal coronary arteries as the control group. ACS patients were divided further into three subgroups: patients with ST-segment elevation myocardial infarction (STEMI) (n=34); patients with non-ST segment elevation myocardial infarction (NSTEMI) (n=29); and patients with unstable angina (n=30). According to their Gensini scores, patients were divided into mild, moderate and severe groups. We compared UA and hs-CRP levels and the relationship with Gensini scores between different groups. RESULTS UA and hs-CRP levels in the ACS group were higher than those in the control group (p < 0.05). UA and hs-CRP levels in the STEMI group were higher than those in the NSTEMI, unstable angina and control groups (p < 0.05). UA and hs-CRP levels in the NSTEMI patients were higher than those in the unstable angina and control groups (p < 0.05). UA and hs-CRP levels in the unstable angina patients were higher than those in the control group (p < 0.05). hs-CRP levels in the STEMI patients were higher than the other groups (p < 0.05). hs-CRP levels in the NSTEMI patients were higher than the unstable angina and the control groups (p < 0.05) while hs-CRP levels in the unstable angina patients were higher than the control group (p < 0.05). Additionally, according to the Gensini score group, we discovered that ACS patients in the severe group had higher hs-CRP levels than the other three groups (p < 0.05) while the moderate group had higher levels than the other two groups (p < 0.05). The mild group had higher levels than the control group (p < 0.05). Correlation analysis suggested that UA levels and Gensini scores had a positive correlation (p < 0.05). hs-CRP levels and Gensini scores also showed a positive correlation (p < 0.05). CONCLUSIONS UA and hs-CRP levels should be considered as factors to use in the risk stratification in ACS patients.
Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis

Significance We report fossil evidence of feather structural protein (beta-keratin) from a 130-My-old basal bird (Eoconfuciusornis) from the famous Early Cretaceous Jehol Biota, which has produced many feathered dinosaurs, early birds, and mammals. Multiple independent molecular analyses of both microbodies and associated matrix recovered from the fossil feathers confirm that these microbodies are indeed melanosomes. We use transmission electron microscopy and immunogold to show localized binding of antibodies raised against feather protein to matrix filaments within these ancient feathers. Our work sheds new light on molecular constituents of tissues preserved in fossils. Microbodies associated with feathers of both nonavian dinosaurs and early birds were first identified as bacteria but have been reinterpreted as melanosomes. Whereas melanosomes in modern feathers are always surrounded by and embedded in keratin, melanosomes embedded in keratin in fossils has not been demonstrated. Here we provide multiple independent molecular analyses of both microbodies and the associated matrix recovered from feathers of a new specimen of the basal bird Eoconfuciusornis from the Early Cretaceous Jehol Biota of China. Our work represents the oldest ultrastructural and immunological recognition of avian beta-keratin from an Early Cretaceous (∼130-Ma) bird. We apply immunogold to identify protein epitopes at high resolution, by localizing antibody–antigen complexes to specific fossil ultrastructures. Retention of original keratinous proteins in the matrix surrounding electron-opaque microbodies supports their assignment as melanosomes and adds to the criteria employable to distinguish melanosomes from microbial bodies. Our work sheds new light on molecular preservation within normally labile tissues preserved in fossils.
Comparison of process parameter optimization using different designs in nanoemulsion-based formulation for transdermal delivery of fullerene

This research aims to formulate and to optimize a nanoemulsion-based formulation containing fullerene, an antioxidant, stabilized by a low amount of mixed surfactants using high shear and the ultrasonic emulsification method for transdermal delivery. Process parameters optimization of fullerene nanoemulsions was done by employing response surface methodology, which involved statistical multivariate analysis. Optimization of independent variables was investigated using experimental design based on Box–Behnken design and central composite rotatable design. An investigation on the effect of the homogenization rate (4,000–5,000 rpm), sonication amplitude (20%–60%), and sonication time (30–150 seconds) on the particle size, ζ-potential, and viscosity of the colloidal systems was conducted. Under the optimum conditions, the central composite rotatable design model suggested the response variables for particle size, ζ-potential, and viscosity of the fullerene nanoemulsion were 152.5 nm, −52.6 mV, and 44.6 pascal seconds, respectively. In contrast, the Box–Behnken design model proposed that preparation under the optimum condition would produce nanoemulsion with particle size, ζ-potential, and viscosity of 148.5 nm, −55.2 mV, and 39.9 pascal seconds, respectively. The suggested process parameters to obtain optimum formulation by both models yielded actual response values similar to the predicted values with residual standard error of <2%. The optimum formulation showed more elastic and solid-like characteristics due to the existence of a large linear viscoelastic region.
FUNCTION OF HISTOCHEMICAL TYPE OF SKELETAL MUSCLE FIBER IN RAT AND MYOSIN HEAVY CHAIN

Objective To analyse and study the distribution of muscle fiber and the composition of myosin heavy chain isoforms(MHCs) in each muscular subvolume of the lateral gastrocnemius of adult SD rats. Methods Succinate dehydrogenase(SDH) staining was applied to analyse the proportions of muscle fibers of four types and sodium dodecyl sulphate-polyacrylamide gel electrophoresis(SDS-PAGE) was also used to measure myosin heavy chain isoforms(MHCs). Results The proportions of types Ⅰ(SO),ⅡX(FO),ⅡA(FOG) and ⅡB(FG) muscle fibers in medial subvolume were(10.2±4.1)%、(2.8±2.1)%、(25.7±9.6)%、(61.3±10.1)% respectively,(15.9±8.2)%、(6.1±2.6)%、(22.8±11.5)%、(55.2±12.6)% in lateral superficial subvolume,(21.3±9.2)%、(9.8±2.5)%、(18.5±8.7)%、(50.4±10.9)% in lateral profound subvolume.The distribution of muscle fibers of four types was of a crisscross and mosaic pattern.Type ⅡX muscle fiber had the smallest transverse area and type ⅡB the biggest,with a medium and a smaller transverse areas for types ⅡA and Ⅰ respectively.They were conformed to MHCs Ⅰ,MHCs Ⅱx,MHCs Ⅱa,MHCs Ⅱb that were separately found in medial subvolume,lateral superficial subvolume and lateral profound subvolume with SDS-PAGE.Conclusion The important function of rat lateral gastrocnemius was flexion of knee joint and extension of ankle joint.The lateral superficial subvolume and the lateral profound subvolume seem to take more part in elevating the calcaneus and small muscular movements,and the medial subvolume plays a role in fast movements when muscular power is needed to a degree greater than 25%.
Endoscopic screening for synchronous esophageal neoplasia among patients with incident head and neck cancer: Prevalence, risk factors, and outcomes

Esophageal squamous‐cell neoplasia (ESCN) is a common second primary neoplasia found in patients with head‐and‐neck squamous‐cell carcinoma (HNSCC). This study sought to identify the risk factors for synchronous ESCN and how they influence survival in HNSCC patient. Eight hundred and fifteen incident HNSCC patients were prospectively recruited for endoscopy screening for ESCN using white‐light imaging, narrow‐band imaging, Lugol chromoendoscopy, and pathological confirmation. Associated lifestyle and clinicopathological data were collected. The interquartile follow‐up period cutoffs were 11.3, 20.5 and 34.9 months. 124 patients (15.2%) were diagnosed as having synchronous ESCN (66 low‐grade dysplasia, 29 high‐grade dysplasia, and 29 esophageal squamous‐cell carcinoma). Consumption of alcohol, but not betel nut or cigarette, was significantly associated with the presence of synchronous ESCN (adjusted odds ratio [aOR] = 7.1 and 10.9 for former and current drinkers, respectively). There was an interaction between cumulative dose of alcohol consumption and alcohol flushing response on the development of ESCN. High‐dose drinkers with flush response were 16.9 times more likely to have esophageal high‐grade dysplasia/SCC than non‐drinkers. Compared with oral cavity cancer patients, those with hypopharyngeal, laryngeal and oropharyngeal cancer were 6.8, 4.6 and 2.8 times more likely to have esophageal high‐grade dysplasia/SCC. HNSCC patients with synchronous ESCN had lower overall survival than those without (p < 0.0001). In conclusion, surveillance of ESCN is strongly recommended for the high‐risk subpopulation of HNSCC patients, especially drinkers who have a flush response to alcohol, and those with distant metastasis of index cancer and cancers in hypopharynx, oropharynx and larynx.
Testing Propositions Derived from Twitter Studies: Generalization and Replication in Computational Social Science

Replication is an essential requirement for scientific discovery. The current study aims to generalize and replicate 10 propositions made in previous Twitter studies using a representative dataset. Our findings suggest 6 out of 10 propositions could not be replicated due to the variations of data collection, analytic strategies employed, and inconsistent measurements. The study’s contributions are twofold: First, it systematically summarized and assessed some important claims in the field, which can inform future studies. Second, it proposed a feasible approach to generating a random sample of Twitter users and its associated ego networks, which might serve as a solution for answering social-scientific questions at the individual level without accessing the complete data archive.
Resistance to RET-Inhibition in RET-Rearranged NSCLC Is Mediated By Reactivation of RAS/MAPK Signaling

Oncogenic rearrangements in RET are present in 1%–2% of lung adenocarcinoma patients. Ponatinib is a multi-kinase inhibitor with low-nanomolar potency against the RET kinase domain. Here, we demonstrate that ponatinib exhibits potent antiproliferative activity in RET fusion–positive LC-2/ad lung adenocarcinoma cells and inhibits phosphorylation of the RET fusion protein and signaling through ERK1/2 and AKT. Using distinct dose escalation strategies, two ponatinib-resistant LC-2/ad cell lines, PR1 and PR2, were derived. PR1 and PR2 cell lines retained expression, but not phosphorylation of the RET fusion and lacked evidence of a resistance mutation in the RET kinase domain. Both resistant lines retained activation of the MAPK pathway. Next-generation RNA sequencing revealed an oncogenic NRAS p.Q61K mutation in the PR1 cell. PR1 cell proliferation was preferentially sensitive to siRNA knockdown of NRAS compared with knockdown of RET, more sensitive to MEK inhibition than the parental line, and NRAS dependence was maintained in the absence of chronic RET inhibition. Expression of NRAS p.Q61K in RET fusion expressing TPC1 cells conferred resistance to ponatinib. PR2 cells exhibited increased expression of EGFR and AXL. EGFR inhibition decreased cell proliferation and phosphorylation of ERK1/2 and AKT in PR2 cells, but not LC-2/ad cells. Although AXL inhibition enhanced PR2 sensitivity to afatinib, it was unable to decrease cell proliferation by itself. Thus, EGFR and AXL cooperatively rescued signaling from RET inhibition in the PR2 cells. Collectively, these findings demonstrate that resistance to ponatinib in RET-rearranged lung adenocarcinoma is mediated by bypass signaling mechanisms that result in restored RAS/MAPK activation. Mol Cancer Ther; 16(8); 1623–33. ©2017 AACR.
Production of marine trematode cercariae: a potentially overlooked path of energy flow in benthic systems

Parasites, in particular trematodes, are unseen but ubiquitous components of marine intertidal ecosystems. Although parasites are known to affect population dynamics and food web structure, their potential function as an unrecognized path of energy flow in these ecosystems is yet to be quantified. We use published data on rates at which trematodes produce free-swimming infec- tive larvae (cercariae) that are released from their gastropod intermediate hosts to investigate patterns in cercarial output as a function of different variables, and to calculate the annual produc- tion of cercariae in different marine benthic systems. Across 18 trematode species, cercarial output (no. cercariae shed snail -1 d -1 ) ranged over 4 orders of magnitude and was positively correlated with snail host species size. While cercarial output did not correlate with latitude, it did correlate nega- tively with the size of cercariae, and was influenced by the type of downstream host sought by cer- cariae, being highest when this host was a vertebrate. Our estimates of annual cercarial production (kJ m -2 yr -1 ), which take into account the density of infected snails in the habitat, were within the range of production values reported for free-living invertebrates inhabiting benthic ecosystems. These estimates would be much higher if they included all trematode species in an ecosystem, and not just single-species values. Overall, results suggest that trematode cercariae represent potentially important paths of energy flow in benthic systems as well as a potentially important food supply to benthic organisms.
Mastering 2048 With Delayed Temporal Coherence Learning, Multistage Weight Promotion, Redundant Encoding, and Carousel Shaping

<italic>2048</italic> is an engaging single-player nondeterministic video puzzle game, which, thanks to the simple rules and hard-to-master gameplay, has gained massive popularity in recent years. As <italic>2048</italic> can be conveniently embedded into the discrete-state Markov decision processes framework, we treat it as a testbed for evaluating existing and new methods in reinforcement learning. With the aim to develop a strong <italic>2048</italic> playing program, we employ temporal difference learning with systematic <inline-formula><tex-math notation="LaTeX">$n$ </tex-math></inline-formula>-tuple networks. We show that this basic method can be significantly improved with temporal coherence learning, multistage function approximator with weight promotion, carousel shaping, and redundant encoding. In addition, we demonstrate how to take advantage of the characteristics of the <inline-formula> <tex-math notation="LaTeX">$n$</tex-math></inline-formula>-tuple network, to improve the algorithmic effectiveness of the learning process by delaying the (decayed) update and applying lock-free optimistic parallelism to effortlessly make advantage of multiple CPU cores. This way, we were able to develop the best known <italic>2048</italic> playing program to date, which confirms the effectiveness of the introduced methods for discrete-state Markov decision problems.