gebhart/patrepeval huggingface dataset:
Molecular sputum analysis for the diagnosis of lung cancer (2013)

Lung cancer is the leading cause of cancer mortality rate worldwide, mainly because of the presence of metastatic disease at the time of diagnosis. Early detection of lung cancer improves prognosis, and towards this end, large screening trials in high-risk individuals have been conducted since the past century. Despite all efforts, the need for novel (complementary) lung cancer diagnostic and screening methods still exists. In this review, we focus on the assessment of lung cancer-related biomarkers in sputum in the past decennium. Besides cytology, mutation and microRNA analysis, special attention has been paid to DNA promoter hypermethylation, of which all available literature is summarised without time restriction. A model is proposed to aid in the distinction between diagnostic and risk markers. Research on the use of sputum for non-invasive detection of early-stage lung cancer has brought new insights and advanced molecular techniques. The sputum shows a promising potential for routine diagnostic and possibly screening purposes.
Action recognition with trajectory-pooled deep-convolutional descriptors (2015)

Visual features are of vital importance for human action understanding in videos. This paper presents a new video representation, called trajectory-pooled deep-convolutional descriptor (TDD), which shares the merits of both hand-crafted features [31] and deep-learned features [24]. Specifically, we utilize deep architectures to learn discriminative convolutional feature maps, and conduct trajectory-constrained pooling to aggregate these convolutional features into effective descriptors. To enhance the robustness of TDDs, we design two normalization methods to transform convolutional feature maps, namely spatiotemporal normalization and channel normalization. The advantages of our features come from (i) TDDs are automatically learned and contain high discriminative capacity compared with those hand-crafted features; (ii) TDDs take account of the intrinsic characteristics of temporal dimension and introduce the strategies of trajectory-constrained sampling and pooling for aggregating deep-learned features. We conduct experiments on two challenging datasets: HMD-B51 and UCF101. Experimental results show that TDDs outperform previous hand-crafted features [31] and deep-learned features [24]. Our method also achieves superior performance to the state of the art on these datasets.
Expression of the Epstein‐Barr virus DNA polymerase in Escherichia coli for use as antigen for the diagnosis of nasopharyngeal carcinoma (1995)

Epstein-Barr virus (EBV) encoded DNA polymerase (POL) was cloned and over-expressed in Escherichia coli. Western blot analysis confirmed the presence of antibody to this POL protein in sera from nasopharyngeal carcinoma (NPC) patients. By Western blot analysis, moderate to high concentration of IgG POL-specific antibodies were present in 43 of 48 NPC sera and only 4 of 48 healthy, seropositive controls. The POL-specific IgG antibodies appear as early as stage I of NPC, suggesting that the recombinant POL protein can be a useful diagnostic marker for early diagnosis of the disease. It was also found that human sera containing high titer of cytomegalovirus (CMV) antibodies or herpes simplex virus type 1 (HSV-1) antibodies did not cross-react with the recombinant EBV POL, despite the homology shared by DNA polymerase proteins of these viruses.
AIDS Therapy: New Push for Clinical Trials (1985)

There is clearly a long way to go before an effective therapy is developed for acquired immunodeficiency syndrome (AIDS). However in the US federal efforts in this area have stepped up in recent months. The US Congress has approved a massive infusion of funds--a budget of US$240 million of which a substantial portion has been earmarked for testing drugs that show some promise against the AIDS virus. The National Institute of Allergy and Infectious Diseases (NIAID) is establishing a network of medical centers to carry out phase II trials of promising compounds that have undergone limited toxicity testing and 2000 patients are expected to be enrolled in these trials by late 1986. In addition to provide coordination and focus to the effort the National Institutes of Health (NIH) has established a drug evaluation committee. 3 major difficulties face AIDS researchers. First the AIDS virus becomes part of the cell it infects suggesting that it may never be removed entirely from the body. Second the virus is now known to infect the brain meaning that drugs must cross the blood-brain barrier. Third even if a drug can be found to interrupt the life cycle of the virus the patients immune system may already have been destroyed indicating a need for additional therapy to reconstitute the immune system. It appears likely that drugs will have to be administered on an intermittent basis throughout an AIDS patients life. Of the 4 compounds currently in limited clinical trials in the US (suramin azidothymidine ribavirin and HPA-23) none seems to offer much clinical improvement when given in the late stages of AIDS. In the future it may be possible to develop drugs that are targeted toward specific features of the life cycle of the AIDS virus. The hope is that if a safe and effective antiviral drug can be given to AIDS patients before their immune systems are destroyed their immune functions may regenerate spontaneously or be reconstituted through additional drug therapy.
DNA As an Adjuvant (2003)

DNA is a complex macromolecule with immunological properties that depend on base sequence. Although mammalian DNA is immunologically inert, DNA from bacteria has potent immunostimulatory properties that result from short sequence motifs called CpG motifs or immunostimulatory sequences (ISS). These motifs, which have the general structure of two 5′ purines, an unmethylated CpG motif, and two 3′ pyrimidines, occur much more commonly in bacterial DNA than mammalian DNA because of two main factors: CpG suppression and the frequent methylation of cytosine in this position in mammalian DNA (1). As a result, bacterial DNA displays (in code-like fashion) sequences emblematic of foreignness. This code allows DNA to function as a danger signal in the induction of innate immunity (2).
Issues of Eco-agricultural Industrialization for Big Qinling Eco-city Cluster (2011)

Firstly, the necessities of ecological agriculture development in Big Qinling Eco-city Cluster were discussed. Then, condition endowment of eco-agricultural industrialization in Big Qinling Eco-city Cluster was analyzed from the aspects of basic conditions and differential endowment of eco-agricultural industrialization. Finally, specific forms and functional orientation of eco-agriculture were pointed out Countermeasures for the eco agricultural industrialization in Big Qinling Eco-city Cluster were put forward. Firstly, the government guidance and the media publicity should be strengthened. Secondly, financial support for the eco-agricultural industrialization in Big Qinling Eco-city Cluster should be enhanced. Thirdly, branding strategies of eco-agricultural products in Big Qinling Eco-city Cluster should be implemented as soon as possible.
Additional file 6: of DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning (2017)

Genomic context. Description of genomic contexts. (XLSX 9Â kb)
The allosteric three-site model for the ribosomal elongation cycle: features and future (1990)

The ribosome contains three binding sites for tRNA, viz., the A site for aminoacyl-tRNA (decoding site), the P site for peptidyl-tRNA, and the E site for deacylated tRNA (E for exit). The surprising finding of an allosteric linkage between the E and A sites in the sense of a negative cooperativity has three consequences: (a) it improves the proper selection of aminoacyl-tRNAs while preventing interference from noncognate aminoacyl-tRNAs in the decoding process, (b) it provides an explanation for the ribosomal accuracy without having to resort to the proofreading hypothesis, and (c) it has deepened our understanding of the mode of action of some antibiotics.
Correlates of Sleep and Waking in Drosophila melanogaster (2000)

Drosophila exhibits a circadian rest-activity cycle, but it is not known whether fly rest constitutes sleep or is mere inactivity. It is shown here that, like mammalian sleep, rest in Drosophila is characterized by an increased arousal threshold and is homeostatically regulated independently of the circadian clock. As in mammals, rest is abundant in young flies, is reduced in older flies, and is modulated by stimulants and hypnotics. Several molecular markers modulated by sleep and waking in mammals are modulated by rest and activity in Drosophila, including cytochrome oxidase C, the endoplasmic reticulum chaperone protein BiP, and enzymes implicated in the catabolism of monoamines. Flies lacking one such enzyme, arylalkylamine N-acetyltransferase, show increased rest after rest deprivation. These results implicate the catabolism of monoamines in the regulation of sleep and waking in the fly and suggest that Drosophila may serve as a model system for the genetic dissection of sleep.
Denoising of stimulated Raman scattering microscopy images via deep learning (2019)

Stimulated Raman scattering (SRS) microscopy is a label-free quantitative chemical imaging technique that has demonstrated great utility in biomedical imaging applications ranging from real-time stain-free histopathology to live animal imaging. However, similar to many other nonlinear optical imaging techniques, SRS images often suffer from low signal to noise ratio (SNR) due to absorption and scattering of light in tissue as well as the limitation in applicable power to minimize photodamage. We present the use of a deep learning algorithm to significantly improve the SNR of SRS images. Our algorithm is based on a U-Net convolutional neural network (CNN) and significantly outperforms existing denoising algorithms. More importantly, we demonstrate that the trained denoising algorithm is applicable to images acquired at different zoom, imaging power, imaging depth, and imaging geometries that are not included in the training. Our results identify deep learning as a powerful denoising tool for biomedical imaging at large, with potential towards <i>in vivo</i> applications, where imaging parameters are often variable and ground-truth images are not available to create a fully supervised learning training set.
siRNA Design Software for a Target Gene-Specific RNA Interference (2012)

RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA suppresses the expression of the intended gene whose transcript possesses perfect complementarity to the siRNA guide strand. Hence, its silencing effect has been assumed to be extremely specific. However, accumulated evidences revealed that siRNA could downregulate unintended genes with partial complementarities mainly to the seven-nucleotide seed region of siRNA. This phenomenon is referred to as off-target effect. We have revealed that the capability to induce off-target effect is strongly correlated to the thermodynamic stability in siRNA seed-target duplex. For understanding accurate target gene function and successful therapeutic application, it may be critical to select a target gene-specific siRNA with minimized off-target effect. Here we present our siRNA design software for a target-specific RNAi. In addition, we also introduce the software programs open to the public for designing functional siRNAs.
Inducing selectivity and chirality in group IV metal coordination with high-denticity hydroxypyridinones (2019)

The solution- and solid-state interactions between the octadentate siderophore mimic 3,4,3-LI(1,2-HOPO) (343HOPO) and group IV metal ions were investigated using high-resolution mass spectrometry, liquid chromatography, UV-visible spectrophotometry, metal-competition batch titrations, and single crystal X-ray diffraction. 343HOPO forms a neutral 1 : 1 complex, [HfIV343HOPO], that exhibits extreme stability in aqueous solution, with a log β110 value reaching 42.3. These results affirm the remarkable charge-based selectivity of 343HOPO for octacoordinated tetravalent cations with a Hf(iv) complex 1021 more stable than its Lu(iii) analogue. Moreover, [HfIV343HOPO] and its Zr(iv) counterpart show exceptional robustness, with the ligand remaining bound to the cation over a very broad pH range: from pH ∼ 11 to acidic conditions as strong as 10 M HCl. In stark contrast, Ti(iv)-343HOPO species are far less stable and undergo hydrolysis at pH as low as ∼6, likely due to the mismatch between the preferred hexacoordinated Ti(iv) ion and octadentate 343HOPO ligand. The extreme charge-based and denticity-driven selectivity of 343HOPO, now observed across the periodic table, paves the way for new selective sequestration systems for radionuclides including medical 44Ti, 89Zr or 177Lu/Hf isotopes, toxic polonium (Po) contaminants, as well as rutherfordium (Rf) research isotopes. Furthermore, despite the lack of a chiral center in 343HOPO, its complexes with metal ions are chiral and appear to form a single set of enantiomers.
Dynamic shim updating (DSU) for multislice signal acquisition (2003)

Dynamic shim updating (DSU) is a technique for achieving optimal magnetic field homogeneity over extended volumes by dynamically updating an optimal shim setting for each individual slice in a multislice acquisition protocol. Here the practical implementation of DSU using all first- and second-order shims is described. In particular, the hardware modifications and software requirements are demonstrated. Furthermore, the temporal effects of dynamically switching shim currents are investigated and a Z(2)-to-Z(0) compensation unit is described and implemented to counteract the temporal Z(0) variations following a change in the Z(2) shim current. The optimal shim settings for all slices are determined with a quantitative and user-independent, multislice phase-mapping sequence. The performance of DSU is evaluated from multislice phase maps and spectroscopic images acquired on rat brain in vivo. DSU improved the magnetic field homogeneity over all spatial slices, with a more pronounced effect on the slices positioned away from the magnet isocenter, thereby making the magnetic field homogeneity highly uniform over an extended volume.
Preoperative Embolization in the Management of Neck Paragangliomas (1997)

Surgery of neck paragangliomas carries inherent risks of excessive blood loss and cranial nerve injury. Preoperative embolization has been used to lessen the morbidity of surgery. We sought to characterize our experience with preoperative embolization by evaluating safety, efficacy, and surgical data. During a period of 22 years (1974 to 1996), 19 consecutive patients with 27 histopathologically confirmed neck paragangliomas were surgically treated at the Oulu University Hospital. All patients underwent preoperative arteriography and 17 patients had cervical ultrasonography (US). Eleven patients with 15 tumors were operated on without embolization and nine patients with 12 tumors were preoperatively embolized with 150- to 250-microm polyvinyl alcohol (PVA) particles. The mean blood loss during surgery in the nonembolized group was 1374 mL (range, 100 to 4500 mL) and the mean operation time was 4 hours and 48 minutes (range, 1.5 to 9 hours). In the embolized group the mean blood loss was significantly less (588 mL; range, 100 to 1800 mL; P = 0.04) and the mean operation time shorter (3 hours 24 minutes; range, 2 to 5 hours; P = 0.05). No embolic complications were recorded after the embolization. We conclude that preoperative embolization of neck paragangliomas 3 cm or greater in diameter with PVA particles is safe. Embolization to minimize operative bleeding facilitates surgery, shortens the operation time, and lessens the surgical risks.
Effect of Two-Year Growth Hormone (GH) Treatment in Children with Non-Endocrine Short Stature (1993)

Sixty-eight children with non-endocrine short stature (NESS) were treated with recombinant human growth hormone (GH) for two years. The patients consisted of 20 children with familial short stature (FSS; Group A), 17 children with small-for-date short stature (SFD; Group B), 5 children with combined FSS and SFD (Group A+B), and 26 children with idiopathic short stature (ISS; Group C). GH treatment significantly increased height velocity, height SD score (SDS), and height velocity SDS for chronological age (CA) in NESS. The mean height velocity was increased by GH treatment from 4.4cm/year to 7.1cm/year in the first year and 6.3cm/year in the second year, the mean height SDS from -3.07 SD to -2.63 SD in the first year and to -2.42 SD in the second year, and the mean height velocity SDS for CA from -1.66 SD to 1.62 SD in the first year and to 0.66 SD in the second year. Among the four groups, there was no significant difference in the effect of GH treatment judged by height velocity or height velocity SDS for CA. However, the treatment tended to be less effective in group A+B. There was no significant difference among the four groups in the increase in height SDS.Seventeen children developed puberty during the two-year GH treatment: 7 in the first year and 10 in the second year. The mean height and age at the onset of puberty in 17 patients were 136.0 (±9.7) cm and 12.23 (±0.86) years in male, and 129.1 (±5.5) cm and 11.3 (±0.7) years in female patients, respectively. The height at the onset of puberty was shorter than that of normal children. Since it is known that children who develop puberty at short stature remain short, it is probable that the patients who developed puberty at short stature in this study will remain short as adults. The effect of treatment evaluated by the height SDS for BA was not improved. The effect of GH treatment in children with NESS should be carefully evaluated by conducting a long-term follow-up.
Characterization of Two VQIXXK Motifs for Tau Fibrillizationin Vitro (2006)

Tau proteins are building blocks of the filaments that form neurofibrillary tangles of Alzheimer's disease (AD) and related neurodegenerative tauopathies. It was recently reported that two VQIXXK motifs in the microtubule (MT) binding region, named PHF6 and PHF6*, are responsible for tau fibrillization. However, the exact role each of these motifs plays in this process has not been analyzed in detail. Using a recombinant human tau fragment containing only the four MT-binding repeats (K18), we show that deletion of either PHF6 or PHF6* affected tau assembly but only PHF6 is essential for filament formation, suggesting a critical role of this motif. To determine the amino acid residues within PHF6 that are required for tau fibrillization, a series of deletion and mutation constructs targeting this motif were generated. Deletion of VQI in either PHF6 or PHF6* lessened but did not eliminate K18 fibrillization. However, removal of the single K311 residue from PHF6 completely abrogated the fibril formation of K18. K311D mutation of K18 inhibited tau filament formation, while K311A and K311R mutations had no effect. These data imply that charge change at position 311 is important in tau fibril formation. A similar requirement of nonnegative charge at this position for fibrillization was observed with the full-length human tau isoform (T40), and data from these studies indicate that the formation of fibrils by T40K311D and T40K311P mutants is repressed at the nucleation phase. These findings provide important insights into the mechanisms of tau fibrillization and suggest targets for AD drug discovery to ameliorate neurodegeneration mediated by filamentous tau pathologies.
The products of pre-B cell-specific genes (lambda 5 and VpreB) and the immunoglobulin mu chain form a complex that is transported onto the cell surface. (1990)

We constructed expression vectors coding for the two pre-B-specific genes, VpreB and lambda 5, and transfected them together with a mu vector (mu tm) into Ig- myeloma cells. In a transfectant expressing all three introduced genes, the mu tm chain is transported on the cell surface. A biochemical analysis demonstrated that, in these cells, the mu tm chain is associated noncovalently with an 18-kD protein and covalently with a 22-kD protein, which are most likely the products of VpreB and lambda 5, respectively. Our results, thus, strongly suggest that the products of lambda 5 and VpreB bind to mu chains and have the same capacity as conventional Ig L chains to allow surface expression of mu chains.
A genome-wide RNAi screen identifies novel targets of neratinib sensitivity leading to neratinib and paclitaxel combination drug treatments (2011)

ErbB2 is frequently activated in tumors, and influences a wide array of cellular functions, including proliferation, apoptosis, cell motility and adhesion. HKI-272 (neratinib) is a small molecule pan-kinase inhibitor of the ErbB family of receptor tyrosine kinases, and shows strong antiproliferative activity in ErbB2-overexpressing breast cancer cells. We undertook a genome-wide pooled lentiviral RNAi screen to identify synthetic lethal or enhancer (synthetic modulator screen) genes that interact with neratinib in a human breast cancer cell line (SKBR-3). These genes upon knockdown would modulate cell viability in the presence of subeffective concentrations of neratinib. We discovered a diverse set of genes whose depletion selectively impaired or enhanced the viability of SKBR-3 cells in the presence of neratinib. We observed diverse pathways including EGFR, hypoxia, cAMP, and protein ubiquitination that, when co-treated with RNAi and neratinib, resulted in arrest of cell proliferation. Examining the changes of these genes and their protein products also led to a rationale for clinically relevant drug combination treatments. Treatment of cells with either paclitaxel or cytarabine in combination with neratinib resulted in a strong antiproliferative effect. The identification of novel mediators of cellular response to neratinib and the development of potential drug combination treatments have expanded our understanding of neratinib's mode-of-action for the development of more effective therapeutic regimens. Notably, our findings support a paclitaxel and neratinib phase III clinical trial in breast cancer patients.
Noise analysis of a combined optical coherence tomograph and a confocal scanning ophthalmoscope (1999)

A fiberized optical coherence tomographic (OCT) system is modified to produce a confocal image similar to that produced by a scanning laser ophthalmoscope. Two possible configurations are presented, one that can deliver either an OCT or a confocal image and another that is capable of producing both the OCT and the confocal images simultaneously. Using the later configuration, we demonstrate such images from the retina in the living eye. The penalty in terms of performance reduction introduced into the optical coherence tomograph when integrated with a confocal receiver and the signal-to-noise ratio analysis for the different confocal receiver configurations are presented.
Chimeric adenoviral vectors incorporating a fiber of human adenovirus 3 efficiently mediate gene transfer into prostate cancer cells (2009)

Of the investigated chimeric HAdV-5/species B vectors, Ad5F3Luc1 was judged to be the most suitable for targeting prostate cancer cells as it showed the highest transductional efficiency in these cells. It is foreseeable that an Ad vector incorporating the HAdV-3 fiber could potentially be used for prostate cancer gene therapy.