Miracle-dz/UniFAR-FTUs huggingface dataset:
Revisiting the vanishing refuge model of diversification

Much of the debate around speciation and historical biogeography has focused on the role of stabilizing selection on the physiological (abiotic) niche, emphasizing how isolation and vicariance, when associated with niche conservatism, may drive tropical speciation. Yet, recent re-emphasis on the ecological dimensions of speciation points to a more prominent role of divergent selection in driving genetic, phenotypic, and niche divergence. The vanishing refuge model (VRM), first described by Vanzolini and Williams (1981), describes a process of diversification through climate-driven habitat fragmentation and exposure to new environments, integrating both vicariance and divergent selection. This model suggests that dynamic climates and peripheral isolates can lead to genetic and functional (i.e., ecological and phenotypic) diversity, resulting in sister taxa that occupy contrasting habitats with abutting distributions. Here, we provide predictions for populations undergoing divergence according to the VRM that encompass habitat dynamics, phylogeography, and phenotypic differentiation across populations. Such integrative analyses can, in principle, differentiate the operation of the VRM from other speciation models. We applied these principles to a lizard species, Coleodactylus meridionalis, which was used to illustrate the model in the original paper. We incorporate data on inferred historic habitat dynamics, phylogeography and thermal physiology to test for divergence between coastal and inland populations in the Atlantic Forest of Brazil. Environmental and genetic analyses are concordant with divergence through the VRM, yet physiological data are not. We emphasize the importance of multidisciplinary approaches to test this and alternative speciation models while seeking to explain the extraordinarily high genetic and phenotypic diversity of tropical biomes.
Information about life expectancy related to obesity is most important to cat owners when deciding whether to act on a veterinarian's weight loss recommendation.

OBJECTIVE To determine the relative importance of information communicated to cat owners during veterinarian-client obesity-related conversations. SAMPLE Cat owner participants recruited via snowball sampling. METHODS A cross-sectional online questionnaire was distributed to cat owners who owned cats of any weight status. A discrete choice experiment design was used to determine the relative importance of obesity-related attributes to cat owners when receiving information from a veterinarian. RESULTS A total of 1,095 questionnaires were analyzed. Participating cat owners resided primarily in Canada and the US. Impact on life expectancy was the most important attribute that would encourage participants to pursue weight management for a cat with obesity (relative importance, 32.66%), followed by change to cost of food (20.40%), future quality of life (20.38%), future mobility (14.40%), and risk of developing diabetes (12.15%). CLINICAL RELEVANCE Findings suggest that cat owners consider the impact on life expectancy to be most important when considering whether to follow a veterinarian's recommendation for their cat to lose weight. When veterinary professionals are communicating about obesity in practice, there is the potential to increase owner engagement in weight management efforts for cats by emphasizing the obesity-related information owners prefer to receive.
Preoperative next-generation sequencing of pancreatic cyst fluid is highly accurate in cyst classification and detection of advanced neoplasia

Objective DNA-based testing of pancreatic cyst fluid (PCF) is a useful adjunct to the evaluation of pancreatic cysts (PCs). Mutations in KRAS/GNAS are highly specific for intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs), while TP53/PIK3CA/PTEN alterations are associated with advanced neoplasia. A prospective study was performed to evaluate preoperative PCF DNA testing. Design Over 43-months, 626 PCF specimens from 595 patients were obtained by endoscopic ultrasound (EUS)-fine needle aspiration and assessed by targeted next-generation sequencing (NGS). Molecular results were correlated with EUS findings, ancillary studies and follow-up. A separate cohort of 159 PCF specimens was also evaluated for KRAS/GNAS mutations by Sanger sequencing. Results KRAS/GNAS mutations were identified in 308 (49%) PCs, while alterations in TP53/PIK3CA/PTEN were present in 35 (6%) cases. Based on 102 (17%) patients with surgical follow-up, KRAS/GNAS mutations were detected in 56 (100%) IPMNs and 3 (30%) MCNs, and associated with 89% sensitivity and 100% specificity for a mucinous PC. In comparison, KRAS/GNAS mutations by Sanger sequencing had a 65% sensitivity and 100% specificity. By NGS, the combination of KRAS/GNAS mutations and alterations in TP53/PIK3CA/PTEN had an 89% sensitivity and 100% specificity for advanced neoplasia. Ductal dilatation, a mural nodule and malignant cytopathology had lower sensitivities (42%, 32% and 32%, respectively) and specificities (74%, 94% and 98%, respectively). Conclusions In contrast to Sanger sequencing, preoperative NGS of PCF for KRAS/GNAS mutations is highly sensitive for IPMNs and specific for mucinous PCs. In addition, the combination of TP53/PIK3CA/PTEN alterations is a useful preoperative marker for advanced neoplasia.
Generalized mosaicing: polarization panorama

We present an approach to image the polarization state of object points in a wide field of view, while enhancing the radiometric dynamic range of imaging systems by generalizing image mosaicing. The approach is biologically inspired, as it emulates spatially varying polarization sensitivity of some animals. In our method, a spatially varying polarization and attenuation filter is rigidly attached to a camera. As the system moves, it senses each scene point multiple times, each time filtering it through a different filter polarizing angle, polarizance, and transmittance. Polarization is an additional dimension of the generalized mosaicing paradigm, which has recently yielded high dynamic range images and multispectral images in a wide field of view using other kinds of filters. The image acquisition is as easy as in traditional image mosaics. The computational algorithm can easily handle nonideal polarization filters (partial polarizers), variable exposures, and saturation in a single framework. The resulting mosaic represents the polarization state at each scene point. Using data acquired by this method, we demonstrate attenuation and enhancement of specular reflections and semi reflection separation in an image mosaic.
Kinetic Modeling of Methylene Blue and Crystal Violet Dyes Adsorption on Alginate-Fixed Water Hyacinth in Single and Binary Systems

Removal of Methylene Blue (MB) and Crystal Violet (CV) dyes from monocomponent and binary aqueous solutions by water hyacinth-E. Crassipes roots fixed on alginate (a low-cost adsorbent) has been investigated. The extent of adsorption was evaluated as a function of solution pH, initial dye concentration, and bead biomass loading. Kinetic sorption data were analysed by widely used models: pseudo-first-order, pseudo-second-order, Elovich, and intraparticle diffusion models. The results showed that pseudo-second-order model better described the biosorption experimental data than the pseudo-first-order kinetic model for both dyes, whilst the Elovich model fitted the biosorption experimental data at lower dye concentrations. The intraparticle diffusion model indicated that sorption of CV and MB was characterized by rapid surface adsorption coupled with slow film diffusion process at higher initial dye concentration and at all initial bead biomass loading. The range of mean free energy values confirmed physical adsorption as the mechanism for dye removal from solution.
Diagnostic assistance using oriented vision system for high velocity tooling machines

The described problem is a diagnostic task which must be solved for high-velocity industrial machine tools. Due to environmentally degraded conditions, direct measurements are not possible. Due to the rapidity of the machine, human intervention is not possible in case it causes positional faults. So, an oriented vision solution is proposed. The degraded conditions are vibrations, projections of water and metal chips, dazzling, etc. In this case, there is only one problem that is unable to achieve a diagnostic solution: is it the right piece in the right place? That is why complementary methods are proposed and presented in this paper to answer this question.
Evidence-based guideline: Clinical evaluation and treatment of transverse myelitis: [RETIRED]

Objective: To assess the evidence for diagnostic tests and therapies for transverse myelitis (TM) and make evidence-based recommendations. Methods: A review of the published literature from 1966 to March 2009 was performed, with evidence-based classification of relevant articles. Recommendations: Level B recommendations: neuromyelitis optica (NMO)–immunoglobulin G (IgG) antibodies should be considered useful to determine TM cause in patients presenting with clinical acute complete transverse myelitis (ACTM) features. The presence of NMO-IgG antibodies (aquaporin-4–specific antibodies) should be considered useful in determining increased TM recurrence risk. Level C recommendations: in suspected TM, distinction between ACTM or acute partial transverse myelitis may be considered useful to determine TM etiology and risk for relapse (more common with APTM). Age and gender may be considered useful to determine etiology in patients presenting with TM syndrome, with spinal infarcts seen more often in older patients and more female than male patients having TM due to multiple sclerosis (MS). Brain MRI characteristics consistent with those of MS may be considered useful to predict conversion to MS after a first partial TM episode. Longer spinal lesions extending over >3 vertebral segments may be considered useful in determining NMO vs MS. CSF examination for cells and oligoclonal bands may be considered useful to determine the cause of the TM syndrome. Plasma exchange may be considered in patients with TM who fail to improve after corticosteroid treatment. Rituximab may be considered in patients with TM due to NMO to decrease the number of relapses. Level U recommendations: there is insufficient evidence to support or refute the efficacy of other TM therapies or the usefulness of ethnicity to determine the cause of a subacute myelopathy. GLOSSARY: ACTM: acute complete transverse myelitis APTM: acute partial transverse myelitis CI: confidence interval IgG: immunoglobulin G MS: multiple sclerosis NMO: neuromyelitis optica OCB: oligoclonal band TM: transverse myelitis
Cancer immunotherapy via combining oncolytic virotherapy with chemotherapy: recent advances

Oncolytic viruses are multifunctional anticancer agents with huge clinical potential, and have recently passed the randomized Phase III clinical trial hurdle. Both wild-type and engineered viruses have been selected for targeting of specific cancers, to elicit cytotoxicity, and also to generate antitumor immunity. Single-agent oncolytic virotherapy treatments have resulted in modest effects in the clinic. There is increasing interest in their combination with cytotoxic agents, radiotherapy and immune-checkpoint inhibitors. Similarly to oncolytic viruses, the benefits of chemotherapeutic agents may be that they induce systemic antitumor immunity through the induction of immunogenic cell death of cancer cells. Combining these two treatment modalities has to date resulted in significant potential in vitro and in vivo synergies through various mechanisms without any apparent additional toxicities. Chemotherapy has been and will continue to be integral to the management of advanced cancers. This review therefore focuses on the potential for a number of common cytotoxic agents to be combined with clinically relevant oncolytic viruses. In many cases, this combined approach has already advanced to the clinical trial arena.
Analysis and design of inductive coupling and transceiver circuit for inductive inter-chip wireless superconnect

A wireless bus for stacked chips was developed by utilizing inductive coupling among them. This paper discusses inductor layout optimization and transceiver circuit design. The inductive coupling is analyzed by a simple equivalent circuit model, parameters of which are extracted by a magnetic field model based on the Biot-Savart law. Given communication distance, transmit power, data rate, and SNR budget, inductor layout size is minimized. Two receiver circuits, signal sensitive and yet noise immune, are designed for inductive nonreturn-to-zero (NRZ) signaling where no signal is transmitted when data remains the same. A test chip was fabricated in 0.35-/spl mu/m CMOS technology. Accuracy of the models is verified. Bit-error rate is investigated for various inductor layouts and communication distance. The maximum data rate is 1.25 Gb/s/channel. Power dissipation is 43 mW in the transmitter and 2.6 mW in the receiver at 3.3 V. If chip thickness is reduced to 30 /spl mu/m in 90-nm device generation, power dissipation will be 1 mW/channel or bandwidth will be 1 Tb/s/mm/sup 2/.
Expression of MicroRNAs in the Urinary Sediment of Patients with IgA Nephropathy

Background: Micro-RNAs (miRNAs) regulate one-third of all protein-coding genes and are fundamental in the pathophysiology of a wide range of diseases. We studied the expression of several miRNA species (miR-200 family, miR-205 and miR-192) in the urinary sediment of patients with IgA nephropathy (IgAN). Methods: We studied 43 patients with biopsy-proven IgAN. Urinary expression of miRNAs was determined and compared to that from 13 healthy controls. Results: The levels of urinary miR-200a, miR-200b and miR-429, but not miR-200c, miR-141, miR-205, or miR-192, were down-regulated in patients with IgAN. Proteinuria significantly correlated with urinary expression of miR-200a (r = −0.483, P < 0.001), miR-200b (r = −0.448, P = 0.001) and miR-429 (r = −0.466, P = 0.001). Baseline renal function significantly correlated with urinary expression of miR-200b (r = 0.512, P < 0.001) and miR-429 (r = 0.425, P = 0.005). Urinary gene expression of ZEB2 inversely correlated with miR-200b (r = −0.321, P = 0.017); and vimentin expression inversely correlated with that of miR-200a (r = −0.360, P = 0.007), miR-200b (r = −0.416, P = 0.002) and miR-429 (r = −0.375, P = 0.005). After 33.4 ± 12.6 months, the rate of renal function decline significantly correlated with urinary expression of miR-200b (r = 0.316, P = 0.034). Conclusions: Urinary expression of miR-200a, miR-200b and miR-429 were down-regulated in patients with IgAN, and the degree of reduction correlated with disease severity and rate of progression. The results suggested that these miRNA species might play important roles in the pathophysiology of IgAN. Further studies are needed to clarify the role of urinary miRNA repression as a non-invasive marker of IgAN.
AN EXPLORATORY ANALYSIS OF FACTORS INFLUENCING STUDENTS DECISIONS TO TAKE ONLINE COURSES

This study attempts to examine the perceptions of college students regarding online/hybrid education, the criteria used for decision making and the drawbacks that may keep students from enrolling in online education. Studies by Thomerson and Smith [15], and by Leonard and Guha [7] demonstrate that there are various characteristics that affect students’ perceptions which were the basis for this study. The main factors collected from previous studies that were analyzed included effectiveness, convenience, and social interaction, and level of difficulty. Data were collected by distributing surveys through the internet. 146 usable questionnaires were returned. Factor analysis was performed based on the surveys returned and significant factors were found. These results lead to the proposal of a research model.
Endomorphin-2 Decreases Excitatory Synaptic Transmission in the Spinal Ventral Horn of the Rat

Motor impairment is one of the serious side-effects of morphine, which is an exogenous agonist of the μ-opioid receptor (MOR) as well as a widely used analgesic drug in clinical practice for chronic pain treatment. Endomorphins (EMs, including EM-1 and EM-2), the most effective and specific endogenous agonists of the MOR, exert more potent analgesia in acute and neuropathic pain than other opiates, such as morphine. Although EMs had fewer side-effects comparing to other opiates, motor impairment was still one unwanted reaction which limited its clinical application. In order to prevent and treat the motor impairment, it is critical to reveal the neural mechanisms underlying such locomotion disorder. The purpose of the present study was to reveal the neural mechanisms underlying the effects of EM-2 on the activity of motoneurons in the spinal ventral horn. First, we examine the distribution of EM-2-immunoreactive (IR) primary afferent fibers and their synaptic connections with the motoneurons innervating the skeletal muscles of the lower limb revealed by sciatic nerve retrograde tracing. The results showed that EM-2-IR fibers and terminals were sparsely observed in lamina IX and they formed symmetric synaptic connections with the motoneurons within lamina IX of the spinal ventral horn. Then, whole-cell patch-clamp technique was used to observe the effects of EM-2 on the spontaneous excitatory postsynaptic current (sEPSC) of motoneurons in lamina IX. The results showed that EM-2 could decrease both the frequency and amplitude of the sEPSC of the motoneurons in lamina IX, which was reversed by the MOR antagonist CTOP. These results indicate that EM-2-IR fibers originated from primary afferent fibers form symmetric synaptic connections with motoneurons innervating skeletal muscles of the lower limbs in lamina IX of the spinal ventral horn and EM-2 might exert inhibitory effects on the activities of these motoneurons through both presynaptic and postsynaptic mechanisms.
Toy gun injuries--more than meets the eye.

At the start of the 1998 Christmas season it was noted that an unusually high number of our patients had sustained injuries caused by toy guns. Prior to this time only a few isolated cases of this nature had been seen. The guns concerned were springloaded air guns made in China and labelled with a variety of names of well-known guns (Fig. 1). They contained a magazine capable of holding several brightly coloured rigid 5 mm plastic balls (Fig. 2). The guns are termed ‘soft ball guns’ by the police service. Arecord was kept of all new patients presenting to Groote Schuur and Red Cross War Memorial Children’s Hospital eye clinics during December 1998 and January 1999. In order to prevent further injuries caused by what appeared to be one of the year’s most wanted Christmas gifts, the mass media including local and national television and newspapers were informed of the damage toy guns can cause. This resulted in widespread publicity concerning the danger of such toys. Interviews with doctors, parents, children and toy traders formed the main content of the stories published. Following this campaign there was a marked decline in new presentations.
Psoralen-induced DNA adducts are substrates for the base excision repair pathway in human cells

Interstrand cross-link (ICL) is a covalent modification of both strands of DNA, which prevents DNA strand separation during transcription and replication. Upon photoactivation 8-methoxypsoralen (8-MOP+UVA) alkylates both strands of DNA duplex at the 5,6-double bond of thymidines, generating monoadducts (MAs) and ICLs. It was thought that bulky DNA lesions such as MAs are eliminated only in the nucleotide excision repair pathway. Instead, non-bulky DNA lesions are substrates for DNA glycosylases and AP endonucleases which initiate the base excision repair (BER) pathway. Here we examined whether BER might be involved in the removal of psoralen–DNA photoadducts. The results show that in human cells DNA glycosylase NEIL1 excises the MAs in duplex DNA, subsequently the apurinic/apyrimidinic endonuclease 1, APE1, removes the 3′-phosphate residue at single-strand break generated by NEIL1. The apparent kinetic parameters suggest that NEIL1 excises MAs with high efficiency. Consistent with these results HeLa cells lacking APE1 and/or NEIL1 become hypersensitive to 8-MOP+UVA exposure. Furthermore, we demonstrate that bacterial homologues of NEIL1, the Fpg and Nei proteins, also excise MAs. New substrate specificity of the Fpg/Nei protein family provides an alternative repair pathway for ICLs and bulky DNA damage.
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs

The comparison of structural subsites in proteins is increasingly relevant to the prediction of their biological function. To address this problem, we present the Match Augmentation algorithm (MA). Given a structural motif of interest, such as a functional site, MA searches a target protein structure for a match: the set of atoms with the greatest geometric and chemical similarity. MA is extremely efficient because it exploits the fact that the amino acids in a structural motif are not equally important to function. Using motif residues ranked on functional significance via the Evolutionary Trace (ET), MA prioritizes its search by initially forming matches with functionally significant residues, then, guided by ET, it augments this partial match stepwise until the whole motif is found. With this hierarchical strategy, MA runs considerably faster than other methods, and almost always identifies matches in homologs known to have cognate functional sites. Second, in order to interpret matches, we further introduce a statistical method using nonparametric density estimation of the frequency distribution of structural matches. Our results show that the hierarchy of functional importance within structural motifs speeds up the search within targets, and points to a new method to score their statistical significance.
Architecting phase change memory as a scalable dram alternative

Memory scaling is in jeopardy as charge storage and sensing mechanisms become less reliable for prevalent memory technologies, such as DRAM. In contrast, phase change memory (PCM) storage relies on scalable current and thermal mechanisms. To exploit PCM's scalability as a DRAM alternative, PCM must be architected to address relatively long latencies, high energy writes, and finite endurance. We propose, crafted from a fundamental understanding of PCM technology parameters, area-neutral architectural enhancements that address these limitations and make PCM competitive with DRAM. A baseline PCM system is 1.6x slower and requires 2.2x more energy than a DRAM system. Buffer reorganizations reduce this delay and energy gap to 1.2x and 1.0x, using narrow rows to mitigate write energy and multiple rows to improve locality and write coalescing. Partial writes enhance memory endurance, providing 5.6 years of lifetime. Process scaling will further reduce PCM energy costs and improve endurance.