Miracle-dz/UniFAR-FTUs huggingface dataset:
Candida glabrata Sepsis in an Immunocompetent Individual: A Case Report

Candidemia is a significant source of systemic fungal infections, with Candida glabrata (C. glabrata) becoming prominent in recent decades. We describe a unique case where postoperative urinary retention and C. glabrata UTI led to invasive fungaemia with bladder necrosis. A 37- year-old previously well nulliparous woman underwent an elective diagnostic laparoscopy, hysteroscopy dilation and curettage, and dye studies for investigation of infertility. She re-presented six days post procedure with C. glabrata urosepsis with a subsequent laparoscopy on day 16 revealing fungal plaques in the bladder, and a large necrotic defect in the bladder dome. The patient was managed with bilateral nephrostomies, a pelvic drain and antifungal therapy. Four weeks post-insertion of the nephrostomies, a cystogram revealed spontaneous closure of bladder defect. The nephrostomies were removed and antibiotics and anti-fungal continued for a month until negative urine cultures were attained. The patient was well four months after discharge with mild urinary symptoms. The literature has reported two cases of candida UTIs resulting in bezoars and bladder rupture, occurring only in immunocompromised patients. This case highlights the challenges of C. glabrata sepsis and its potential for severe morbidity in a nonimmunocompromised patient, suggesting the need for guidelines in the early detection and treatment of C. glabrata sepsis.
What do Deep Networks Like to See?

We propose a novel way to measure and understand convolutional neural networks by quantifying the amount of input signal they let in. To do this, an autoencoder (AE) was fine-tuned on gradients from a pre-trained classifier with fixed parameters. We compared the reconstructed samples from AEs that were fine-tuned on a set of image classifiers (AlexNet, VGG16, ResNet-50, and Inception v3) and found substantial differences. The AE learns which aspects of the input space to preserve and which ones to ignore, based on the information encoded in the backpropagated gradients. Measuring the changes in accuracy when the signal of one classifier is used by a second one, a relation of total order emerges. This order depends directly on each classifier's input signal but it does not correlate with classification accuracy or network size. Further evidence of this phenomenon is provided by measuring the normalized mutual information between original images and auto-encoded reconstructions from different fine-tuned AEs. These findings break new ground in the area of neural network understanding, opening a new way to reason, debug, and interpret their results. We present four concrete examples in the literature where observations can now be explained in terms of the input signal that a model uses.
Time-domain homogenization of bianisotropic media

In this paper we propose a time-domain homogenization technique for complex media. By using the periodic unfoldin g method and the finite element method, we simulate the electromagnetic behaviour of a composite bianisotropic material and compute its homogenized electromagnetic parameters. In particular, numerical results are obtained for a Debye-like bianisotropic material.
Association between IGF 2 BP 2 polymorphisms and type 2 diabetes mellitus : A case-control study and meta-analysis

Background: Genome-wide association studies (GWAS) found that IGF2BP2 rs4402960 and rs1470579 polymorphisms were associated with type 2 diabetes mellitus (T2DM) risk. Many studies have replicated this association, but yielded inconsistent results. Materials and Methods: A case-control study consisting of 461 T2DM patients and 434 health controls was conducted to detect the genetic susceptibility of IGF2BP2 in a northern Han Chinese population. A meta-analysis was to evaluate the association more precisely in Asians. Results: In the case-control study, the carriers of TT genotype at rs4402960 had a higher T2DM risk than the G carriers (TG + GG) (adjusted odd ratio (AOR) = 1.962, 95% confidence interval (95% CI) = 1.065–3.612, p = 0.031]; CC carriers at rs1470579 were more susceptible to T2DM than A carriers (CA + AA) (AOR = 2.014, 95% CI = 1.114–3.642, p = 0.021). The meta-analysis containing 36 studies demonstrated that the two polymorphisms were associated with T2DM under the allele comparison, genetic models of dominant and recessive in Asians (p < 0.05). The rs4402960 polymorphisms were significantly associated with the T2DM risk after stratification by diagnostic criterion, size of sample and average age and BMI of cases, while there’re no consistent results for rs1470579. Conclusions: Our data suggests that IGF2BP2 polymorphisms are associated with T2DM in Asian populations.
Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.
SRSF7 knockdown promotes apoptosis of colon and lung cancer cells

Serine/arginine-rich (SR) proteins are a family of important splicing factors, which are involved in multiple aspects of RNA processing, including splicing, mRNA nuclear export, mRNA stability and translation. Previous studies have identified a number of SR proteins that exhibit abnormal expression in various tumor types. In the present study, the expression and function of serine/arginine-rich splicing factor 7 (SRSF7) were investigated in colon and lung cancer. Using tissue immunohistochemistry, it was observed that SRSF7 was overexpressed in colon and lung cancer tissues. As the role of SRSF7 in cancer remains to be fully elucidated, the expression of SRSF7 was knocked down in the present study by transfecting SRSF7-specific small interfering RNAs (siRNAs) into the HCT116 colon cancer cell line and A549 lung cancer cell line, which exhibited elevated expression of SRSF7. MTS assays, western blot analysis, flow cytometry and spectrofluorometer analyses were performed to assess the effects of SRSF7 knockdown on the proliferation and apoptosis of cells. The results demonstrated that the expression of SRSF7 was efficiently knocked down by SRSF7 siRNA, and that SRSF7 knockdown inhibited proliferation and enhanced apoptosis of HCT116 and A549 cells. Further experiments involving BEAS-2B cells stably overexpressing SRSF7, and A549 cells with stable knockdown of SRSF7 revealed that SRSF7 regulated the splicing of the apoptosis regulator Fas. Collectively, these data indicated that SRSF7 is critical for the survival of colon and lung cancer cells, and may be a potential therapeutic target for the treatment of colon and lung cancer.
Auditory Input Shapes Tonotopic Differentiation of Kv1.1 Expression in Avian Cochlear Nucleus during Late Development

Tonotopic differentiation is fundamental for signal processing in the auditory system. However, when and how this differentiation arises remain elusive. We addressed this issue using electrophysiology and immunohistochemistry in nucleus magnocellularis of chickens of both sexes, which is known to differ in the expression of Kv1.1 channels depending on characteristic frequency (CF). Just after hearing onset (embryonic day 12–14), Kv1 current gradually increased to a slightly larger extent in neurons with higher CF, causing a tonotopic difference of Kv1 current before hatch. However, after hatch, a much larger increase of Kv1 current occurred, particularly in higher-CF neurons, due to an augmentation of Kv1.1 expression at the plasma membrane. This later change in expression led to the large tonotopic difference of Kv1 current characteristic of mature animals. Attenuation of auditory input by inducing conductive or sensorineural hearing loss around hatch suppressed the differentiation in a level-dependent manner. Moreover, elevation of auditory input during embryonic periods could not reproduce the differentiation, suggesting that the capacity of neurons to drive Kv1.1 expression via auditory input develops in a cell-specific manner, thus underlying the frequency-specific expression of the channel within the nucleus. The results indicated that the tonotopic differentiation of Kv1.1 in nucleus magnocellularis is partially determined before hatch, but largely driven by afferent input after hatch. Our results highlight the importance of neuronal capacity for sound to drive ion channel expression as well as the level of auditory experience in the frequency tuning of brainstem auditory circuits. SIGNIFICANCE STATEMENT Tuning-frequency-specific expression of ion channels is a prerequisite for auditory system function, but its underlying mechanisms remain unclear. Here, we revealed in avian cochlear nucleus that the expression of Kv1.1 became more dependent on auditory input at a late period of maturation in neurons tuned to higher-frequency sound, leading to frequency-specific Kv1.1 expression. Attenuation of auditory input during this period suppressed the differentiation in a level-dependent manner, whereas elevation of input in earlier periods could not reproduce the differentiation. Thus, the capacity of neurons to drive Kv1.1 expression via auditory input develops in a cell-specific manner and directs differentiation, highlighting the importance of neuronal character as well as the level of input in the frequency tuning of auditory circuits.
Teaching computer networking fundamentals using practical laboratory exercises

Motivating students to learn computer networking concepts is often difficult because many students find the subject rather technical, dry, and boring. To overcome this problem, the author has prepared some practical laboratory exercises (practicals) and other materials. They are designed around a network operating system and a multiuser, multitasking operating system and are suitable for classroom use in undergraduate computer networking courses. The effectiveness of these practicals has been evaluated both formally by students and informally in discussion within the teaching team. The implementation of the practicals was judged to be successful because of the positive student feedback and also because students scored better in the final exam. This paper describes the practicals, their overall effectiveness, and plans for further projects. The impact of practicals on student learning and comprehension is also discussed
The Secretome and N-Glycosylation Profiles of the Charophycean Green Alga, Penium margaritaceum, Resemble Those of Embryophytes

The secretome can be defined as the population of proteins that are secreted into the extracellular environment. Many proteins that are secreted by eukaryotes are N-glycosylated. However, there are striking differences in the diversity and conservation of N-glycosylation patterns between taxa. For example, the secretome and N-glycosylation structures differ between land plants and chlorophyte green algae, but it is not clear when this divergence took place during plant evolution. A potentially valuable system to study this issue is provided by the charophycean green algae (CGA), which is the immediate ancestors of land plants. In this study, we used lectin affinity chromatography (LAC) coupled with mass spectrometry to characterize the secretome including secreted N-glycoproteins of Penium margaritaceum, which is a member of the CGA. The identified secreted proteins and N-glycans were compared to those known from the chlorophyte green alga Chlamydomonas reinhardtii and the model land plant, Arabidopsis thaliana, to establish their evolutionary context. Our approach allowed the identification of cell wall proteins and proteins modified with N-glycans that are identical to those of embryophytes, which suggests that the P. margaritaceum secretome is more closely related to those of land plants than to those of chlorophytes. The results of this study support the hypothesis that many of the proteins associated with plant cell wall modification as well as other extracellular processes evolved prior to the colonization of terrestrial habitats.
Lung Rest During Extracorporeal Membrane Oxygenation for Neonatal Respiratory Failure—Practice Variations and Outcomes

Objective: Describe practice variations in ventilator strategies used for lung rest during extracorporeal membrane oxygenation for respiratory failure in neonates, and assess the potential impact of various lung rest strategies on the duration of extracorporeal membrane oxygenation and the duration of mechanical ventilation after decannulation. Data Sources: Retrospective cohort analysis from the Extracorporeal Life Support Organization registry database during the years 2008–2013. Study Selection: All extracorporeal membrane oxygenation runs for infants less than or equal to 30 days of life for pulmonary reasons were included. Data Extraction: Ventilator type and ventilator settings used for lung rest at 24 hours after extracorporeal membrane oxygenation initiation were obtained. Data Synthesis: A total of 3,040 cases met inclusion criteria. Conventional mechanical ventilation was used for lung rest in 88% of cases and high frequency ventilation was used in 12%. In the conventional mechanical ventilation group, 32% used positive end-expiratory pressure strategy of 4–6 cm H2O (low), 22% used 7–9 cm H2O (mid), and 43% used 10–12 cm H2O (high). High frequency ventilation was associated with an increased mean (SEM) hours of extracorporeal membrane oxygenation (150.2 [0.05] vs 125 [0.02]; p < 0.001) and an increased mean (SEM) hours of mechanical ventilation after decannulation (135 [0.09] vs 100.2 [0.03]; p = 0.002), compared with conventional mechanical ventilation among survivors. Within the conventional mechanical ventilation group, use of higher positive end-expiratory pressure was associated with a decreased mean (SEM) hours of extracorporeal membrane oxygenation (high vs low: 136 [1.06] vs 156 [1.06], p = 0.001; mid vs low: 141 [1.06] vs 156 [1.06]; p = 0.04) but increased duration of mechanical ventilation after decannulation in the high positive end-expiratory pressure group compared with low positive end-expiratory pressure (p = 0.04) among survivors. Conclusions: Wide practice variation exists with regard to ventilator settings used for lung rest during neonatal respiratory extracorporeal membrane oxygenation. Use of high frequency ventilation when compared with conventional mechanical ventilation and use of low positive end-expiratory pressure strategy when compared with mid positive end-expiratory pressure and high positive end-expiratory pressure strategy is associated with longer duration of extracorporeal membrane oxygenation. Further research to provide evidence to drive optimization of pulmonary management during neonatal respiratory extracorporeal membrane oxygenation is warranted.
Named Entity Recognition for Telugu News Articles using Naïve Bayes Classifier

The Named Entity Recognition (NER) is identifying name of Person, Location, Organization etc. in a given sentence or a document. In this paper, we have attempted to classify textual content from on-line Telugu newspapers using well known generative model. We have used generic features like contextual words and their part-of-speech (POS) to build the learning model. By understanding the syntax and grammar of Telugu language, we propose morphological pre-processing of the data and this step yields us better accuracy. We propose some interesting language dependent features like post-position feature, clue word feature and gazetteer feature to improve the performance of the model. The model achieved an overall average F1-Score of 88.87% for Person, 87.32% for Location and 72.69% for Organization.
CUNY Academic Works

The dynamics and in ﬂ uence of fake news on Twitter during the 2016 US presidential election remains to be clari ﬁ ed. Here, we use a dataset of 171 million tweets in the ﬁ ve months preceding the election day to identify 30 million tweets, from 2.2 million users, which contain a link to news outlets. Based on a classi ﬁ cation of news outlets curated by www.opensources. co, we ﬁ nd that 25% of these tweets spread either fake or extremely biased news. We characterize the networks of information ﬂ ow to ﬁ nd the most in ﬂ uential spreaders of fake and traditional news and use causal modeling to uncover how fake news in ﬂ uenced the presidential election. We ﬁ nd that, while top in ﬂ uencers spreading traditional center and left leaning news largely in ﬂ uence the activity of Clinton supporters, this causality is reversed for the fake news: the activity of Trump supporters in ﬂ uences the dynamics of the top fake news spreaders.
Emotional Development in Adults with Autism and Intellectual Disabilities: A Retrospective, Clinical Analysis

Individuals with intellectual disability (ID) are at risk for additional autism spectrum disorders (ASD). A large amount of research reveals deficits in emotion-related processes that are relevant to social cognition in ASD. However, studies on the structure and level of emotional development (ED) assessing emotional maturity according to the normative trajectory in typically developing children are scares. The level of ED can be evaluated by the ‘Scheme of Appraisal of Emotional Development’ (SAED), a semi-structured interview with a close caregiver. The SAED assesses the level of emotional developmental based on a five stage system in 10 domains, for example, ‘interaction with peers’ or ‘object permanence’, which are conducive to the overall emotional developmental level. This study examined the ED as measured by the SAED in 289 adults (mean age: 36 years) with ID with and without additional ASD. A lower level in ED was observed in ASD/ID combined that corresponded to the ED of typically developing children aged 1.5–3 years versus an ED with a corresponding age of 3–7 years in ID individuals without ASD. Moreover, distinct strengths in ‘object permanence’, and weaknesses in ‘interaction’, ‘verbal communication’, ‘experience of self’, ‘affect differentiation’, ‘anxiety’, and ‘handling of material objects’ led to a characteristic pattern of ED in ASD. SAED domains with highest discriminative power between ID individuals with and without ASD (5/10) were used to predict ASD group membership. The classification using a selection of SAED domains revealed a sensitivity of 77.5% and a specificity of 76.4%. ASD risk increased 2.7-fold with every SAED level. The recognition of delayed and uneven pattern of ED contributes to our understanding of the emotion-related impairments in adults with ID and ASD these individuals. Assessment of intra-individual ED could add value to the standard diagnostic procedures in ID, a population at risk for underdiagnosed ASD.
ICTV Virus Taxonomy Profile: Asfarviridae.

The family Asfarviridae includes the single species African swine fever virus, isolates of which have linear dsDNA genomes of 170-194 kbp. Virions have an internal core, an internal lipid membrane, an icosahedral capsid and an outer lipid envelope. Infection of domestic pigs and wild boar results in an acute haemorrhagic fever with transmission by contact or ingestion, or by ticks of the genus Ornithodoros. Indigenous pigs act as reservoirs in Africa, where infection is endemic, and from where introductions occur periodically to Europe. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Asfarviridae, which is available at www.ictv. global/report/asfarviridae.
Subjective Simulation as a Notion of Morphism for Composing Concurrent Resources

Recent approaches to verifying programs in separation logics for concurrency have used state transition systems (STSs) to specify the atomic operations of programs. A key challenge in the setting has been to compose such STSs into larger ones, while enabling programs specified under one STS to be linked to a larger one, without reverification. This paper develops a notion of morphism between two STSs which permits such lifting. The morphisms are a constructive form of simulation between the STSs, and lead to a general and concise proof system. We illustrate the concept and its generality on several disparate examples, including staged construction of a readers/writers lock and its proof, and of proofs about quiescence when concurrent programs are executed without external interference.
Opportunistic synergy: a classifier fusion engine for micro-gesture recognition

In this paper, we present a novel opportunistic paradigm for in-vehicle gesture recognition. This paradigm allows using two or more subsystems in a synergistic manner: they can work in parallel but the lack of some of them does not compromise the functioning of the whole system. In order to segment and recognize micro-gestures performed by the user on the steering wheel, we combine a wearable approach based on the electromyography of the user's forearm muscles, with an environmental approach based on pressure sensors integrated directly on the steering wheel. We present and analyze several fusion methods and gesture segmentation strategies. A prototype has been developed and evaluated with data from nine subjects. The results prove that the proposed opportunistic system performs equal or better than each stand-alone subsystem while increasing the interaction possibilities.
Massive MIMO and mmWave for 5 G Wireless HetNet

Date of publication: 1 February 2016 There has been active research worldwide to develop the next-generation, i.e., fifth-generation (5G), wireless network. The 5G network is expected to support a significantly large amount of mobile data traffic and a huge number of wireless connections and achieve better costand energy-efficiency as well as quality of service (QoS) in terms of communication delay, reliability, and security. To this end, the 5G wireless network should exploit the potential of new developments, including superdense and heterogeneous deployment of cells and massive antenna arrays [i.e., massive Potential Benefits and Challenges