gebhart/patrepeval huggingface dataset:
Design and Screening of M13 Phage Display cDNA Libraries (2011)

The last decade has seen a steady increase in screening of cDNA expression product libraries displayed on the surface of filamentous bacteriophage. At the same time, the range of applications extended from the identification of novel allergens over disease markers to protein-protein interaction studies. However, the generation and selection of cDNA phage display libraries is subjected to intrinsic biological limitations due to their complex nature and heterogeneity, as well as technical difficulties regarding protein presentation on the phage surface. Here, we review the latest developments in this field, discuss a number of strategies and improvements anticipated to overcome these challenges making cDNA and open reading frame (ORF) libraries more readily accessible for phage display. Furthermore, future trends combining phage display with next generation sequencing (NGS) will be presented.
Engineered nanoparticles interacting with cells: size matters (2014)

With the rapid advancement of nanoscience and nanotechnology, detailed knowledge of interactions between engineered nanomaterials and cells, tissues and organisms has become increasingly important, especially in regard to possible hazards to human health. This review intends to give an overview of current research on nano-bio interactions, with a focus on the effects of NP size on their interactions with live cells. We summarize common techniques to characterize NP size, highlight recent work on the impact of NP size on active and passive cellular internalization and intracellular localization. Cytotoxic effects are also discussed.
High Through-Plane Thermal Conduction of Graphene Nanoflake Filled Polymer Composites Melt-Processed in an L-Shape Kinked Tube (2015)

Design of materials to be heat-conductive in a preferred direction is a crucial issue for efficient heat dissipation in systems using stacked devices. Here, we demonstrate a facile route to fabricate polymer composites with directional thermal conduction. Our method is based on control of the orientation of fillers with anisotropic heat conduction. Melt-compression of solution-cast poly(vinylidene fluoride) (PVDF) and graphene nanoflake (GNF) films in an L-shape kinked tube yielded a lightweight polymer composite with the surface normal of GNF preferentially aligned perpendicular to the melt-flow direction, giving rise to a directional thermal conductivity of approximately 10 W/mK at 25 vol % with an anisotropic thermal conduction ratio greater than six. The high directional thermal conduction was attributed to the two-dimensional planar shape of GNFs readily adaptable to the molten polymer flow, compared with highly entangled carbon nanotubes and three-dimensional graphite fillers. Furthermore, our composite with its density of approximately 1.5 g/cm(3) was mechanically stable, and its thermal performance was successfully preserved above 100 °C even after multiple heating and cooling cycles. The results indicate that the methodology using an L-shape kinked tube is a new way to achieve polymer composites with highly anisotropic thermal conduction.
Endoplasmic Reticulum Stress Interacts With Inflammation in Human Diseases (2015)

The endoplasmic reticulum (ER) is a critical organelle for normal cell function and homeostasis. Disturbance in the protein folding process in the ER, termed ER stress, leads to the activation of unfolded protein response (UPR) that encompasses a complex network of intracellular signaling pathways. The UPR can either restore ER homeostasis or activate pro-apoptotic pathways depending on the type of insults, intensity and duration of the stress, and cell types. ER stress and the UPR have recently been linked to inflammation in a variety of human pathologies including autoimmune, infectious, neurodegenerative, and metabolic disorders. In the cell, ER stress and inflammatory signaling share extensive regulators and effectors in a broad spectrum of biological processes. In spite of different etiologies, the two signaling pathways have been shown to form a vicious cycle in exacerbating cellular dysfunction and causing apoptosis in many cells and tissues. However, the interaction between ER stress and inflammation in many of these diseases remains poorly understood. Further understanding of the biochemistry, cell biology, and physiology may enable the development of novel therapies that spontaneously target these pathogenic pathways.
Real-time bacterial microcolony counting using on-chip microscopy (2016)

Observing microbial colonies is the standard method for determining the microbe titer and investigating the behaviors of microbes. Here, we report an automated, real-time bacterial microcolony-counting system implemented on a wide field-of-view (FOV), on-chip microscopy platform, termed ePetri. Using sub-pixel sweeping microscopy (SPSM) with a super-resolution algorithm, this system offers the ability to dynamically track individual bacterial microcolonies over a wide FOV of 5.7 mm × 4.3 mm without requiring a moving stage or lens. As a demonstration, we obtained high-resolution time-series images of S. epidermidis at 20-min intervals. We implemented an image-processing algorithm to analyze the spatiotemporal distribution of microcolonies, the development of which could be observed from a single bacterial cell. Test bacterial colonies with a minimum diameter of 20 μm could be enumerated within 6 h. We showed that our approach not only provides results that are comparable to conventional colony-counting assays but also can be used to monitor the dynamics of colony formation and growth. This microcolony-counting system using on-chip microscopy represents a new platform that substantially reduces the detection time for bacterial colony counting. It uses chip-scale image acquisition and is a simple and compact solution for the automation of colony-counting assays and microbe behavior analysis with applications in antibacterial drug discovery.
LncRNA DANCR upregulates PI3K/AKT signaling through activating serine phosphorylation of RXRA (2018)

Conventional therapies and novel molecular targeted therapies against breast cancer have gained great advances over the past two decades. However, poor prognosis and low survival rate are far from expectation for improvement, particularly in patients with triple negative breast cancer (TNBC). Here, we found that lncRNA DANCR was significantly overregulated in TNBC tissues and cell lines compared with normal breast tissues or other type of breast cancer. Knockdown of DANCR suppressed TNBC proliferation both in vitro and in vivo. Further study of underlying mechanisms demonstrated that DANCR bound with RXRA and increased its serine 49/78 phosphorylation via GSK3β, resulting in activating PIK3CA transcription, and subsequently enhanced PI3K/AKT signaling and TNBC tumorigenesis. Taken together, Our findings identified DANCR as an pro-oncogene and uncoverd a new working pattern of lncRNA to mediate TNBC tumorigenesis, which may be a potential therapeutic target for improving treatment of TNBC.
Reliability of PCR decontamination systems. (1994)

A major problem in the application of PCR is contamination with material amplified previously. Repeated PCRs result in the accumulation of intact and degraded amplicons and primer artifacts that can contaminate following amplification reactions. Post-PCR UV treatment and pre-PCR uracil DNA glycosylase (UDG) digestion have been recognized to efficiently inactivate or decompose intact amplification fragments. We show here that degraded amplification products and primer artifacts account for decreased sensitivity and may cause false-negative results. Our experiments indicate that partly degraded PCR products and primer artifacts containing sequences homologous to the primer oligonucleotides in the succeeding PCR reaction compete efficiently with sample DNA for the primers. The experiments done in this study may explain unexpectedly low PCR sensitivities reported in an increasing number of publications. In an attempt to solve this problem, we evaluated three post-PCR treatment methods to completely eliminate sequences competing for the amplification primers, namely, 8-methoxypsoralen (MOPS) or hydroxylamine treatment of amplified DNA and use of oligonucleotides containing 5'-ChemiClamps. However, all three methods did not sufficiently inhibit artificially produced carryover contaminations. In conclusion, false-positive results can be eliminated with UDG or UV treatment, but physical barriers are indispensable to avoid the occurrence of false-negative results.
Humor in Word Embeddings: Cockamamie Gobbledegook for Nincompoops (2019)

While humor is often thought to be beyond the reach of Natural Language Processing, we show that several aspects of single-word humor correlate with simple linear directions in Word Embeddings. In particular: (a) the word vectors capture multiple aspects discussed in humor theories from various disciplines; (b) each individual's sense of humor can be represented by a vector, which can predict differences in people's senses of humor on new, unrated, words; and (c) upon clustering humor ratings of multiple demographic groups, different humor preferences emerge across the different groups. Humor ratings are taken from the work of Engelthaler and Hills (2017) as well as from an original crowdsourcing study of 120,000 words. Our dataset further includes annotations for the theoretically-motivated humor features we identify.
Design of PID controller for sun tracker system using QRAWCP approach (2017)

In this paper, a direct formula is proposed for design of robust PID controller for sun tracker system using quadratic regulator approach with compensating pole (QRAWCP). The main advantage of the proposed approach is that, there is no need to use recently developed iterative soft computing techniques which are time consuming, computationally inefficient and also there is need to know boundary of search space. In order to show the superiority of the proposed approach, performance of the sun tracker system is compared with the recently applied tuning approaches for sun tracker systems such as particle swarm optimization, firefly algorithm and cuckoo search algorithm. The performance of the existing and proposed approaches are verified in time domain, frequency domain and also using integral performances indices. It is found that the performance is improved in transient, robustness, and uncertainty aspects in comparison to recently proposed soft computing approaches.
Formal description of data conversion algorithms for automatic synthesis (2002)

This paper discusses the formal description of data conversion algorithms using a functional description language for automatic synthesis. The translation into an SFG representation is performed in order to identify the analog and digital partitions and then recognize possible circuit structures to implement the algorithm. The achieved representation allows an extension of the automatic synthesis of data conversion systems to a higher abstraction level and can lead to a generalized synthesis environment for data conversion systems.
An improved performance of copper phthalocyanine OFETs with channel and source/drain contact modifications (2015)

We report an effective method to improve the performance of p-type copper phthalocyanine (CuPc) based organic field-effect transistors (OFETs) by employing a thin para-quaterphenyl (p-4p) film and simultaneously applying V2O5 to the source/drain regions. The p-4p layer was inserted between the insulating layer and the active layer, and V2O5 layer was added between CuPc and Al in the source–drain (S/D) area. As a result, the field-effect saturation mobility and on/off current ratio of the optimized device were improved to 5 × 10−2 cm2/(V·s) and 104, respectively. We believe that because p-4p could induce CuPc to form a highly oriented and continuous film, this resulted in the better injection and transport of the carriers. Moreover, by introducing the V2O5 electrode's modified layers, the height of the carrier injection barrier could be effectively tuned and the contact resistance could be reduced.
Crowd detection and occupancy estimation through indirect environmental measurements (2014)

In this paper, the real-time estimation of indoor occupancy has been evaluated starting from the processing of environmental parameters. The proposed system is based on a low cost and non-invasive wireless sensor network infrastructure for the distributed acquisition of simple quantities like temperature and humidity. The proposed algorithm has been structured in three successive phases of detection, filtering, and classification in order to face with the high variability and instability of such quantities. The problem of occupancy estimation has been recast as an inverse problem solved by means of a customized learning-by-example strategy (i.e., the classification phase). A measurement campaign in a museum area has been carried out and preliminary experimental results have been obtained in order to assess the potentialities and limitations of the proposed strategy.
Overexpression of OsRAN2 in rice and Arabidopsis renders transgenic plants hypersensitive to salinity and osmotic stress (2009)

Nucleo-cytoplasmic partitioning of regulatory proteins is increasingly being recognized as a major control mechanism for the regulation of signalling in plants. Ras-related nuclear protein (Ran) GTPase is required for regulating transport of proteins and RNA across the nuclear envelope and also has roles in mitotic spindle assembly and nuclear envelope (NE) assembly. However, thus far little is known of any Ran functions in the signalling pathways in plants in response to changing environmental stimuli. The OsRAN2 gene, which has high homology (77% at the amino acid level) with its human counterpart, was isolated here. Subcellular localization results showed that OsRan2 is mainly localized in the nucleus, with some in the cytoplasm. Transcription of OsRAN2 was reduced by salt, osmotic, and exogenous abscisic acid (ABA) treatments, as determined by real-time PCR. Overexpression of OsRAN2 in rice resulted in enhanced sensitivity to salinity, osmotic stress, and ABA. Seedlings of transgenic Arabidopsis thaliana plants overexpressing OsRAN2 were overly sensitive to salinity stress and exogenous ABA treatment. Furthermore, three ABA- or stress-responsive genes, AtNCED3, AtPLC1, and AtMYB2, encoding a key enzyme in ABA synthesis, a phospholipase C homologue, and a putative transcriptional factor, respectively, were shown to have differentially induced expression under salinity and ABA treatments in transgenic and wild-type Arabidopsis plants. OsRAN2 overexpression in tobacco epidermal leaf cells disturbed the nuclear import of a maize (Zea mays L.) leaf colour transcription factor (Lc). In addition, gene-silenced rice plants generated via RNA interference (RNAi) displayed pleiotropic developmental abnormalities and were male sterile.
Current State of Text Sentiment Analysis from Opinion to Emotion Mining (2017)

Sentiment analysis from text consists of extracting information about opinions, sentiments, and even emotions conveyed by writers towards topics of interest. It is often equated to opinion mining, but it should also encompass emotion mining. Opinion mining involves the use of natural language processing and machine learning to determine the attitude of a writer towards a subject. Emotion mining is also using similar technologies but is concerned with detecting and classifying writers emotions toward events or topics. Textual emotion-mining methods have various applications, including gaining information about customer satisfaction, helping in selecting teaching materials in e-learning, recommending products based on users emotions, and even predicting mental-health disorders. In surveys on sentiment analysis, which are often old or incomplete, the strong link between opinion mining and emotion mining is understated. This motivates the need for a different and new perspective on the literature on sentiment analysis, with a focus on emotion mining. We present the state-of-the-art methods and propose the following contributions: (1) a taxonomy of sentiment analysis; (2) a survey on polarity classification methods and resources, especially those related to emotion mining; (3) a complete survey on emotion theories and emotion-mining research; and (4) some useful resources, including lexicons and datasets.
Distinctions in the specificity of E2F function revealed by gene expression signatures (2005)

The E2F family of transcription factors provides essential activities for coordinating the control of cellular proliferation and cell fate. Both E2F1 and E2F3 proteins have been shown to be particularly important for cell proliferation, whereas the E2F1 protein has the capacity to promote apoptosis. To explore the basis for this specificity of function, we used DNA microarray analysis to probe for the distinctions in the two E2F activities. Gene expression profiles that distinguish either E2F1- or E2F3-expressing cells from quiescent cells are enriched in genes encoding cell cycle and DNA replication activities, consistent with many past studies. E2F1 profile is also enriched in genes known to function in apoptosis. We also identified patterns of gene expression that specifically differentiate the activity of E2F1 and E2F3; this profile is enriched in genes known to function in mitosis. The specificity of E2F function has been attributed to protein interactions mediated by the marked box domain, and we now show that chimeric E2F proteins generate expression signatures that reflect the origin of the marked box, thus linking the biochemical mechanism for specificity of function with specificity of gene activation.
The Preparation of Matrine Liposome and Its Antiglioma Activity Study (2014)

The aim of the study was to study the preparation of matrine liposome and its activity for resisting cells, to study the preparation of matrine liposome by orthogonal design, and to observe the inhibiting effect of matrine on glioma through MTT method, Flow Cytometer, and electron microscope. The results showed that we take the encapsulation efficiency as the index; the optimal preparation of matrine liposome is 100 mg of lecithin, 40 mg of cholesterol, phosphate buffered saline (PBS) with pH value 6.4, and 40 mg of matrine. The result of MTT testing is shown that the tested group with medium and high dosage (0.75, 1.0, 1.25 mg/L) of matrine has significant inhibiting rate to the growth of BT 325 cells. The<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi>A</mml:mi></mml:mrow></mml:math>value in tested group with medium and high dosage is up to<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mn>0.19</mml:mn><mml:mo>±</mml:mo><mml:mn>0.03</mml:mn></mml:math>. The methods of Flow Cytometer and electron microscope prove that matrine can inhibit the growth of BT 325 cells. Matrine is active in inhibiting brain glioma.
Universal Use of Intraoperative Nerve Monitoring by Recently Fellowship‐Trained Thyroid Surgeons is Common, Associated with Higher Surgical Volume, and Impacts Intraoperative Decision‐Making (2015)

A survey of recently trained endocrine and head and neck surgeons reveals that the vast majority (95 %) of these surgeons commonly use IONM during thyroid surgery. IONM was more commonly used by higher-volume surgeons. Routine users were more likely to modify surgery based on nerve integrity (i.e., not complete a total thyroidectomy if the nerve loses conduction signal).
Ecological Impacts of the Deepwater Horizon Oil Spill: Implications for Immunotoxicity (2011)

The Deepwater Horizon (DWH) oil spill was the largest environmental disaster and response effort in U.S. history, with nearly 800 million liters of crude oil spilled. Vast areas of the Gulf of Mexico were contaminated with oil, including deep-ocean communities and over 1,600 kilometers of shoreline. Multiple species of pelagic, tidal, and estuarine organisms; sea turtles; marine mammals; and birds were affected, and over 20 million hectares of the Gulf of Mexico were closed to fishing. Several large-scale field efforts were performed, including assessments of shoreline and wildlife oiling and of coastal waters and sediments. The assessment of injuries, damages, and restoration options for the DWH spill is ongoing. Although petroleum and the polycyclic aromatic hydrocarbon component of oils are known to affect the immune systems of aquatic organisms and wildlife, immunotoxicity is not typically assessed during oil spills and has not been a focus of the DHW assessment. The effects of oil spill contaminants on immune responses are variable and often exposure dependent, but immunotoxic effects seem likely from the DHW spill based on the reported effects of a variety of oils on both aquatic and wildlife species.
The Permeability of Human Oral Mucosa and Skin to Water (1989)

Specimens from four regions of oral mucosa (palate, buccal mucosa, lateral border of the tongue, and the floor of the mouth) and of abdominal skin were taken from 58 individuals at autopsy, for determination of permeability constants (Kp) to tritium-labeled water. Comparisons between fresh specimens and those stored at -80 degrees C revealed no significant effect on Kp as a result of freezing; similar results were found with use of specimens from corresponding regions of the pig. Values for Kp were significantly different for all of the tissue regions examined and ranged from 44 +/- 4 x 10(-7) cm/min for skin to 973 +/- 33 x 10(-7) cm/min for the floor of the mouth, which was the most permeable region. Similar differences were evident among corresponding regions of porcine oral mucosa and skin. Moreover, the Kp values obtained for human tissues were not significantly different from those of the pig, except for the floor of the mouth, which was more permeable in human than in pig tissue. The results reveal interesting differences in the permeability of human oral mucosa that might be related to susceptibility to mucosal disease in those conditions where local extrinsic etiological agents are implicated.
Circulating MicroRNA223 is a New Biomarker for Inflammatory Bowel Disease (2016)

Endoscopy is an important tool in screening and monitoring inflammatory bowel disease (IBD); however, it is invasive, costly, and associated with risks to the patients. Recently, circulating microRNAs (miRNAs) have emerged as promising noninvasive biomarkers. We proposed that the expression of serum microRNA223 (miR-223) could be a biomarker for IBD.Studies were conducted using serum samples from 100 patients with IBD (50 with Crohn's disease [CD] and 50 with ulcerative colitis [UC]) and 50 healthy controls. The expression of serum miR-223 was measured by quantitative reverse transcription-polymerase chain reaction. The clinical disease activity was assessed by measurement of the Crohn's disease activity index for CD and the Mayo score for UC. Endoscopies were performed and graded according to the simple endoscopic score for CD and the ulcerative colitis endoscopic index of severity scores for UC. Blood samples for the measurement of high-sensitivity C-reactive protein (hs-CRP) and erythrocyte sedimentation rate (ESR) were taken within 1 week before or after endoscopy.Serum miR-223 expression increased 2.2 times in patients with CD and 2.8 times in patients with UC compared with the control group. Most importantly, the level of serum miR-223 was correlated with several indicators of disease activity both in CD and UC. Serum miR-223 demonstrated a higher Spearman r value than ESR and hs-CRP in detecting the disease activity of patients with IBD.Serum miR-223 might be a promising biomarker for monitoring disease activity in IBD patients.