gebhart/patrepeval huggingface dataset:
Auto-directed video stabilization with robust L1 optimal camera paths (2011)

We present a novel algorithm for automatically applying constrainable, L1-optimal camera paths to generate stabilized videos by removing undesired motions. Our goal is to compute camera paths that are composed of constant, linear and parabolic segments mimicking the camera motions employed by professional cinematographers. To this end, our algorithm is based on a linear programming framework to minimize the first, second, and third derivatives of the resulting camera path. Our method allows for video stabilization beyond the conventional filtering of camera paths that only suppresses high frequency jitter. We incorporate additional constraints on the path of the camera directly in our algorithm, allowing for stabilized and retargeted videos. Our approach accomplishes this without the need of user interaction or costly 3D reconstruction of the scene, and works as a post-process for videos from any camera or from an online source.
Correlations between the percentage of tumor cells showing an anaplastic lymphoma kinase (ALK) gene rearrangement, ALK signal copy number, and response to crizotinib therapy in ALK fluorescence in situ hybridization–positive nonsmall cell lung cancer (2012)

The strong association between increased copy number of key ALK signals and percentage of positive cells suggests that the <100% rate of cellular positivity in ALK+ tumors is due to technical factors, not biological factors. In ALK+ tumors, neither the percentage of positive cells nor signal copy number appear to be informative variables for predicting benefit from ALK inhibition. The inverse relationship between fused and isolated red copy number suggests ALK+ may be a distinct "near-diploid" subtype of NSCLC that develops before significant chromosomal aneusomy occurs.
Circadian Rhythms, Melatonin and Depression (2011)

The master biological clock situated in the suprachiasmatic nuclei of the anterior hypothalamus plays a vital role in orchestrating the circadian rhythms of multiple biological processes. Increasing evidence points to a role of the biological clock in the development of depression. In seasonal depression and in bipolar disorders it seems likely that the circadian system plays a vital role in the genesis of the disorder. For major unipolar depressive disorder (MDD) available data suggest a primary involvement of the circadian system but further and larger studies are necessary to conclude. Melatonin and melatonin agonists have chronobiotic effects, which mean that they can readjust the circadian system. Seasonal affective disorders and mood disturbances caused by circadian malfunction are theoretically treatable by manipulating the circadian system using chronobiotic drugs, chronotherapy or bright light therapy. In MDD, melatonin alone has no antidepressant action but novel melatoninergic compounds demonstrate antidepressant properties. Of these, the most advanced is the novel melatonin agonist agomelatine, which combines joint MT1 and MT2 agonism with 5-HT(2C) receptor antagonism. Adding a chronobiotic effect to the inhibition of 5-HT(2C) receptors may explain the rapid impact of agomelatine on depression, since studies showed that agomelatine had an early impact on sleep quality and alertness at awakening. Further studies are necessary in order to better characterize the effect of agomelatine and other novel melatoninergic drugs on the circadian system of MDD patients. In summary, antidepressants with intrinsic chronobiotic properties offer a novel approach to treatment of depression.
A Novel Microchip Nitric Oxide Sensor with sub-nM Detection Limit (2002)

Since the discovery of nitric oxide (NO) as a vasodilatory messenger, in particular after its identification as an endothelial-derived relaxing factor (EDRF), there has been a mushroom effect in the research of NO in biological systems. Monitoring of NO in biological samples in vivo and in real time is desirable in many fields of NO research. Although several techniques are available for measurement of NO, the electrochemical method is most advantageous because of its speed and sensitivity. Since the first commercially available electrochemical NO detection system, many NO electrodes have been developed with dimensions from μm to cm, and with detection limits in the low nanomolar range. However, there is still a continuing demand for new NO sensors with lower detection limits. An electrochemical sensor to detect nitric oxide gas dissolved in solution as well as in gas phase is described as well as a fabrication method for the electrode. The sensor is based on the selective oxidation of nitric oxide by a multielectrode array of microelectrodes created on activated carbon, which has been deposited on a silicon chip substrate. The array, in turn, is further modified with several layers of cationic ion exchanger then the subsequent addition of NO selective membranes. The microchip NO sensor, is characterized by a linear response to concentrations of NO up to 100 μM, a response time of a few seconds, and a detection limit of less than 0.3 nM. In biological samples the sensor discriminates against substances such as nitrite, dopamine and ascorbic acid. Moreover, compared with present NO sensors, this sensor is significantly less temperature sensitive, resulting in significantly improved sensor detectivity as compared with present electrochemical sensors. Major applications for measurement of NO concentration are in chemical media, biological tissue, cell cultures, or in blood.
Reduction of Pentylenetetrazole-Induced Seizure Activity in Awake Rats by Seizure-Triggered Trigeminal Nerve Stimulation (2000)

Stimulation of the vagus nerve has become an effective method for desynchronizing the highly coherent neural activity typically associated with epileptic seizures. This technique has been used in several animal models of seizures as well as in humans suffering from epilepsy. However, application of this technique has been limited to unilateral stimulation of the vagus nerve, typically delivered according to a fixed duty cycle, independently of whether ongoing seizure activity is present. Here, we report that stimulation of another cranial nerve, the trigeminal nerve, can also cause cortical and thalamic desynchronization, resulting in a reduction of seizure activity in awake rats. Furthermore, we demonstrate that providing this stimulation only when seizure activity begins results in more effective and safer seizure reduction per second of stimulation than with previous methods. Seizure activity induced by intraperitoneal injection of pentylenetetrazole was recorded from microwire electrodes in the thalamus and cortex of awake rats while the infraorbital branch of the trigeminal nerve was stimulated via a chronically implanted nerve cuff electrode. Continuous unilateral stimulation of the trigeminal nerve reduced electrographic seizure activity by up to 78%, and bilateral trigeminal stimulation was even more effective. Using a device that automatically detects seizure activity in real time on the basis of multichannel field potential signals, we demonstrated that seizure-triggered stimulation was more effective than the stimulation protocol involving a fixed duty cycle, in terms of the percent seizure reduction per second of stimulation. In contrast to vagus nerve stimulation studies, no substantial cardiovascular side effects were observed by unilateral or bilateral stimulation of the trigeminal nerve. These findings suggest that trigeminal nerve stimulation is safe in awake rats and should be evaluated as a therapy for human seizures. Furthermore, the results demonstrate that seizure-triggered trigeminal nerve stimulation is technically feasible and could be further developed, in conjunction with real-time seizure-predicting paradigms, to prevent seizures and reduce exposure to nerve stimulation.
Engineered Conformation-dependent VEGF Peptide Mimics Are Effective in Inhibiting VEGF Signaling Pathways (2011)

Angiogenesis, or formation of new blood vessels, is crucial to cancer tumor growth. Tumor growth, progression, and metastasis are critically influenced by the production of the pro-angiogenic vascular endothelial growth factor (VEGF). Promising anti-angiogenic drugs are currently available; however, their susceptibilities to drug resistance and long term toxicity are serious impediments to their use, thus requiring the development of new therapeutic approaches for safe and effective angiogenic inhibitors. In this work, peptides were designed to mimic the VEGF-binding site to its receptor VEGFR-2. The VEGF conformational peptide mimic, VEGF-P3(CYC), included two artificial cysteine residues, which upon cyclization constrained the peptide in a loop native-like conformation to better mimic the anti-parallel structure of VEGF. The engineered cyclic VEGF mimic peptide demonstrated the highest affinity to VEGFR-2 by surface plasmon resonance assay. The VEGF peptide mimics were evaluated as inhibitors in several in vitro assays in which VEGF-dependent signaling pathways were observed. All VEGF mimics inhibited VEGFR-2 phosphorylation with VEGF-P3(CYC) showing the highest inhibitory effects when compared with unstructured peptides. Additionally, we show in several angiogenic in vitro assays that all the VEGF mimics inhibited endothelial cell proliferation, migration, and network formation with the conformational VEGF-P3 (CYC) being the best. The VEGF-P3(CYC) also caused a significant delay in tumor development in a transgenic model of VEGF(+/-)Neu2-5(+/-). These results indicate that the structure-based design is important for the development of this peptidomimetic and for its anti-angiogenic effects.
Network management: Emerging trends and challenges (2002)

Network management is arguably one of the most important challenges faced by the owners and operators of advanced networks and services. Lucent Technologies, as a major equipment vendor, and Bell Labs, as its R&D arm, have had extensive historical experience with designing network management systems for AT&T telecommunication networks and other associated data networks. This experience enables Lucent to provide unique differentiation to its products and also places it in an excellent position to address the network management needs and challenges of the emerging networks and services. This issue of the Bell Labs Technical Journal provides a sample of some of the many the activities, tools, technology trends, and designs currently under way in network management in various wings of Lucent. This paper, an introduction to the issue, discusses the evolution of network management, placing it in the context of underlying networking trends. In addition, it provides a brief introduction to the papers presented in this issue, which together provide a snapshot of Lucent's network management activities in support of an efficient, reliable, and flexible networking vision.
Lipopeptides from Staphylococcus aureus as Tlr2 Ligands: Prediction with mRNA Expression, Chemical Synthesis, and Immunostimulatory Activities (2009)

Recognize this? Based on predictions from mRNA expression of lipoproteins from Staphylococcus aureus, lipopeptide fragments were chemically synthesized, and their TLR2-stimulatory activities and cytokine-induction capabilities were analyzed. All the lipopeptides activated TLR2, but the activities varied depending on their peptide sequences.
THE PRESERVATION AND CLINICAL USE OF FREEZE-DRIED BONE (1951)

1. Freeze-dried homogenous bone grafts measuring 6 to 8 centimeters by 0.5 to 1.0 centimeter were grafted into the radii of dogs. It was found that they were incorporated in the same manner as fresh autogenous bone grafts but at a slightly slower rate. The freeze-dried bone was somewhat superior to frozen bone in regard to the rate of healing in the early phases. 2. Except for the previously mentioned variations in the rate of healing, all the grafts were incorporated in a manner roughhy comparable to the healing of the bone defect of the same size in which grafts were not inplanted. 3. The advantages of storage at room temperatures, the potentiallY increased storage periods, the case of transportation, and initial clinical success suggest that freeze-dried homogenous bone is suitable for use in bone banks.
Disposable Microdevices for DNA Analysis and Cell Sorting (1998)

We have developed microfabricated devices to size and sort microscopic objects, based on measurement of fluorescent properties. With these devices, we have demonstrated sizing and sorting on various biological entities, ranging from E. Coli cells to single molecules of DNA. The microfabricated devices have several advantages over macroscopic systems, including size, cost and sensitivity. For example, the detection volume for our devices is 375 femtoliters, more than an order of magnitude smaller than what has been achieved with flow cytometry.
Changes in Clinical and Physiologic Variables Predict Survival in Idiopathic Pulmonary Fibrosis (2003)

There is significant heterogeneity in survival time among patients with idiopathic pulmonary fibrosis. Studies of baseline clinical and physiologic variables as predictors of survival time have reported inconsistent results. We evaluated the predictive value of changes in clinical and physiologic variables over time for survival time in 81 patients with biopsy-proven idiopathic pulmonary fibrosis. Six-month changes in dyspnea score, total lung capacity, thoracic gas volume, FVC, FEV1, diffusing capacity of carbon monoxide, partial pressure of arterial oxygen, oxygen saturation, and alveolar-arterial oxygen gradient were predictive of survival time even after adjustment for baseline values. Analyses were repeated on 51 patients with 12-month change data. Twelve-month changes in dyspnea score, total lung capacity, FVC, partial pressure of arterial oxygen, oxygen saturation, and alveolar-arterial oxygen gradient were predictive of survival time after adjustment for baseline values. Evaluation of changes in clinical and physiological variables over 6 and 12 months may provide clinicians with more accurate prognostic information than baseline values alone.
Enhanced Adhesion by Gecko-Inspired Hierarchical Fibrillar Adhesives (2009)

The complex structures that allow geckos to repeatably adhere to surfaces consist of multilevel branching fibers with specialized tips. We present a novel technique for fabricating similar multilevel structures from polymer materials and demonstrate the fabrication of arrays of two- and three-level structures, wherein each level terminates in flat mushroom-type tips. Adhesion experiments are conducted on two-level fiber arrays on a 12-mm-diameter glass hemisphere, which exhibit both increased adhesion and interface toughness over one-level fiber samples and unstructured control samples. These adhesion enhancements are the result of increased surface conformation as well as increased extension during detachment.
High-power rod-type photonic crystal fiber laser (2005)

We report on a novel ytterbium-doped fiber design that combines the advantages of rod and fiber gain media. The fiber design has outer dimensions of a rod laser, meaning a diameter in the range of a few millimeters and a length of just a few tens of centimeters, and includes two important waveguide structures, one for pump radiation and one for laser radiation. We obtained 120-W output power in single-mode beam quality from a 48-cm-long fiber cane that corresponds to an extracted power of 250 W/m. The fiber has significantly reduced nonlinearity, which therefore allows for scalability in the performance of a high-peak-power fiber laser and amplifier system.
Real‐Time Monitoring of Luminal Esophageal Temperature During Left Atrial Radiofrequency Catheter Ablation for Atrial Fibrillation: Observations About Esophageal Heating During Ablation at the Pulmonary Vein Ostia and Posterior Left Atrium (2006)

Real-time monitoring of luminal esophageal position and temperature is feasible, enhances recognition of esophageal heating, and may add useful information beyond that provided by fluoroscopic assessment of esophageal position. There is a potential role for esophageal monitoring to help avoid thermal injury to the esophagus during catheter ablation for atrial fibrillation.
Human Multidrug Resistance ABCB and ABCG Transporters: Participation in a Chemoimmunity Defense System (2006)

In this review we give an overview of the physiological functions of a group of ATP binding cassette (ABC) transporter proteins, which were discovered, and still referred to, as multidrug resistance (MDR) transporters. Although they indeed play an important role in cancer drug resistance, their major physiological function is to provide general protection against hydrophobic xenobiotics. With a highly conserved structure, membrane topology, and mechanism of action, these essential transporters are preserved throughout all living systems, from bacteria to human. We describe the general structural and mechanistic features of the human MDR-ABC transporters and introduce some of the basic methods that can be applied for the analysis of their expression, function, regulation, and modulation. We treat in detail the biochemistry, cell biology, and physiology of the ABCB1 (MDR1/P-glycoprotein) and the ABCG2 (MXR/BCRP) proteins and describe emerging information related to additional ABCB- and ABCG-type transporters with a potential role in drug and xenobiotic resistance. Throughout this review we demonstrate and emphasize the general network characteristics of the MDR-ABC transporters, functioning at the cellular and physiological tissue barriers. In addition, we suggest that multidrug transporters are essential parts of an innate defense system, the "chemoimmunity" network, which has a number of features reminiscent of classical immunology.
Changes in behavior and gene expression induced by caloric restriction in C57BL/6 mice (2009)

Caloric restriction (CR) is an effective method for prevention of age-associated diseases as well as overweight and obesity; however, there is controversy regarding the effects of dieting regimens on behavior. In this study, we investigated two different dieting regimens: repeated fasting and refeeding (RFR) and daily feeding of half the amount of food consumed by RFR mice (CR). CR and RFR mice had an approximate 20% reduction in food intake compared with control mice. Open field, light-dark transition, elevated plus maze, and forced swimming tests indicated that CR, but not RFR, reduced anxiety- and depressive-like behaviors, with a reduction peak on day 8. Using a mouse whole genome microarray, we analyzed gene expression in the prefrontal cortex, amygdala, and hypothalamus. In addition to the CR-responsive genes commonly modified by RFR and CR, each regimen differentially changed the expression of distinct genes in each region. The most profound change was observed in the amygdalas of CR mice: 884 genes were specifically upregulated. Ingenuity pathway analysis revealed that these 884 genes significantly modified nine canonical pathways in the amygdala. alpha-Adrenergic and dopamine receptor signalings were the two top-scoring pathways. Quantitative RT-PCR confirmed the upregulation of six genes in these pathways. Western blotting confirmed that CR specifically increased dopamine- and cAMP-regulated phosphoprotein (Darpp-32), a key regulator of dopamine receptor signaling, in the amygdala. Our results suggest that CR may change behavior through altered gene expression.
Robust isolation of malignant plasma cells in multiple myeloma (2014)

Molecular characterization of malignant plasma cells is increasingly important for diagnostic and therapeutic stratification in multiple myeloma. However, the malignant plasma cells represent a relatively small subset of bone marrow cells, and need to be enriched prior to analysis. Currently, the cell surface marker CD138 (SDC1) is used for this enrichment, but has an important limitation in that its expression decreases rapidly after sampling. Seeking alternatives to CD138, we performed a computational screen for myeloma plasma cell markers and systematically evaluated 7 candidates. Our results conclusively show that the markers CD319 (SLAMF7/CS1) and CD269 (TNFRSF17/BCMA) are considerably more robust than CD138 and enable isolation of myeloma plasma cells under more diverse conditions, including the samples that have been delayed or frozen. Our results form the basis of improved procedures for characterizing cases of multiple myeloma in clinical practice.
N6‐(Carbamoylmethyl)‐2′‐deoxyadenosine, a rare DNA Constituent: Phosphoramidite Synthesis and Properties of Palindromic Dodecanucleotides (1987)

Abstract N 6 ‐(Carbamoylmethyl)‐2′‐deoxyadenosine ( 1 ), a modified nucleoside occurring in bacteriophage Mu, was synthesized by two different routes. Glycinamide was introdued by nucleophilic displacement of(2,4,6,‐triisopro‐pylphenyl)sulfonyloxy or ethylsulfinyl groups at C(6) of the purine moiety. Compound 1 was converted into the protected phosphoramidite 6b and employed in solid‐phase synthesis of the self‐complementary oligonucleotides 7–14 . Replacement of 2′‐deoxyadenosine by 1 led to a strong decrease of the T m values of the oligomers d(A‐T) 6 ( 7 ) and d(A‐T‐G‐A‐A‐G‐C‐T‐T‐C‐A‐T)( 10 ), respectively. As the oligemer 10 contains the recognition site d(A‐A‐G‐C‐T‐T) of the endodeoxyribonuclease Hind III, it was subjected to sequence‐specific hydrolysis experiments. Replacement of the first or second A d by 1 prevented enzymatic phosphodiester hydrolysis (results with 11 and 12 ). In contrast, slow hydrolysis was observed if the less bulky N 6 ‐methyl‐2′‐deoxyadenosine replaced the second A d residue (results with 14 ).
DNA vaccination by mecA sequence evokes an antibacterial immune response against methicillin-resistant Staphylococcus aureus (1999)

More than 90% of methicillin-resistant Staphylococcus aureus (MRSA) isolates produce a penicillin-binding protein PBP2' (or PBP2a) with low affinity for beta-lactam antibiotics. PBP2' is encoded by the mecA gene, a foreign gene integrated into the chromosome of methicillin-susceptible S. aureus (MSSA). DNA vaccination by injection of transgene-expressing plasmids has been demonstrated to elicit an immune response against transgene-encoded protein. We hypothesized that the application of DNA vaccination with the mecA sequence would elicit protective immunity against MRSA. This immunity was evoked by injection of a mecA-expressing plasmid into BALB/c mice. Anti-PBP2' antibody was detected in the sera obtained from the DNA-vaccinated mice. These sera produced a five-fold increase in phagocytosis of MRSA compared with sera from mice treated with control plasmid. However, there was no difference in phagocytosis of MSSA among these groups. In addition, the in-vivo antibacterial effect of DNA vaccination was demonstrated in mice infected with MRSA. Eight days after iv inoculation of 10(8) cfu of MRSA into mice, the number of bacteria in the kidneys obtained from mice vaccinated with mecA-expressing plasmid (1.48 +/- 0.27 x 10(5) cfu/mg kidney; n = 18) was significantly lower than that from mice vaccinated with negative control plasmid (3.59 +/- 0.57 x 10(5) cfu/mg kidney; n = 17) (P < 0.02) or that from sham-treated mice (3. 43 +/- 0.66 x 10(5) cfu/mg kidney; n = 9) (P < 0.02). Interestingly, PBP2' was found in both the bacterial membrane fraction and the supernatant, thus being accessible to serum antibodies. Together these observations indicate that PBP2' or the mecA sequence may be eligible as a candidate molecule for vaccination against MRSA.
Vancomycin levels after intravitreal injection. Effects of inflammation and surgery. (1995)

Clearance of vancomycin from the phakic eye is prolonged compared to that of beta-lactam antibiotics, an important pharmacokinetic advantage in treating endophthalmitis. Its clearance from aphakic-vitrectomized eyes is dramatically faster than from phakic eyes and is similar to that of other antimicrobial agents.