gebhart/patrepeval huggingface dataset:
A paper-based, cell-free biosensor system for the detection of heavy metals and date rape drugs (2019)

Biosensors have emerged as a valuable tool with high specificity and sensitivity for fast and reliable detection of hazardous substances in drinking water. Numerous substances have been addressed using synthetic biology approaches. However, many proposed biosensors are based on living, genetically modified organisms and are therefore limited in shelf life, usability and biosafety. We addressed these issues by the construction of an extensible, cell-free biosensor. Storage is possible through freeze drying on paper. Following the addition of an aqueous sample, a highly efficient cell-free protein synthesis (CFPS) reaction is initiated. Specific allosteric transcription factors modulate the expression of 'superfolder' green fluorescent protein (sfGFP) depending on the presence of the substance of interest. The resulting fluorescence intensities are analyzed with a conventional smartphone accompanied by simple and cheap light filters. An ordinary differential equitation (ODE) model of the biosensors was developed, which enabled prediction and optimization of performance. With an optimized cell-free biosensor based on the Shigella flexneri MerR transcriptional activator, detection of 6 μg/L Hg(II) ions in water was achieved. Furthermore, a completely new biosensor for the detection of gamma-hydroxybutyrate (GHB), a substance used as date-rape drug, was established by employing the naturally occurring transcriptional repressor BlcR from Agrobacterium tumefaciens.
Assessment of folate receptor alpha and beta expression in selection of lung and pancreatic cancer patients for receptor targeted therapies (2017)

A number of folate receptor (FR) targeted small molecular drugs and monoclonal antibodies have been introduced into clinical trials to treat FR positive cancers. Because the therapeutic efficacy of these drugs depends prominently on the level of FR-α expression on the cancer cells, patients have been commonly selected for FR-targeted therapies based on the intensity of a folate-targeted radioimaging agent. Unfortunately, uptake of such imaging agents can be mediated by both major isoforms of the folate receptor, FR-α and FR-β. Logically, if the FR positive cell population in a tumor mass is dominated by FR-β positive macrophages, patients could be selected for therapy that have few FR-expressing cancer cells. Although several IHC studies have examined expression of either FR-α or FR-β, no study to date has investigated expression of both FR-α and FR-β in the same tumor mass. Herein, we utilize monoclonal antibodies specific for FR-α (mAb343) and FR-β (m909) to query each isoform's expression in a range of cancers. We show that lung and pancreatic adenocarcinomas express the full spectrum of FR-α and FR-β combinations with ~76% of lung adenocarcinomas expressing both FR-α and FR-β while pancreatic cancers express primarily FR-β. Thus, while folate-targeted imaging of lung cancer patients might accurately reflect the expression of FR-α on lung cancer cells, imaging of pancreatic cancer patients could mislead a physician into treating a nonresponding patient. Overall, these data suggest that an independent analysis of both FR-α and FR-β should be obtained to predict the potential efficacy of a folate-targeted drug.
Extraction of Food Consumption Systems by Nonnegative Matrix Factorization (NMF) for the Assessment of Food Choices (2011)

In Western countries where food supply is satisfactory, consumers organize their diets around a large combination of foods. It is the purpose of this article to examine how recent nonnegative matrix factorization (NMF) techniques can be applied to food consumption data to understand these combinations. Such data are nonnegative by nature and of high dimension. The NMF model provides a representation of consumption data through latent vectors with nonnegative coefficients, that we call consumption systems (CS), in a small number. As the NMF approach may encourage sparsity of the data representation produced, the resulting CS are easily interpretable. Beyond the illustration of its properties we provide through a simple simulation result, the NMF method is applied to data issued from a French consumption survey. The numerical results thus obtained are displayed and thoroughly discussed. A clustering based on the k-means method is also achieved in the resulting latent consumption space, to recover food consumption patterns easily usable for nutritionists.
Precorrelation Filter Design for Spread-Spectrum Code Tracking in Interference (1985)

Optimal design of a precorrelation filtering system for use in noncoberent direct-sequence code-tracking loops in the presence of colored noise is described, utilizing a linearized theory of loop operation. The design produces a bias-free loop with an odd S-curve, for which the rms tracking error is minimized. As a byproduct, one arm of the tracking loop provides an optimized signal for data-detection purposes. Widely applicable performance calculations, including rms tracking jitter, mean time to lose lock, and average detection signal-to-noise ratio, are given and illustrated, based on nonlinear models of loop operation.
Visual Memorability for Robotic Interestingness Prediction via Unsupervised Online Learning (2020)

In this paper, we explore the problem of interesting scene prediction for mobile robots. This area is currently underexplored but is crucial for many practical applications such as autonomous exploration and decision making. Inspired by industrial demands, we first propose a novel translation-invariant visual memory for recalling and identifying interesting scenes, then design a three-stage architecture of long-term, short-term, and online learning. This enables our system to learn human-like experience, environmental knowledge, and online adaption, respectively. Our approach achieves much higher accuracy than the state-of-the-art algorithms on challenging robotic interestingness datasets.
Biopsy Techniques for Melanoma (2015)

Abstract In 2014, the incidence of cutaneous melanoma in the United States was 76,100, making it the fifth most common malignancy in males and seventh amongst females. Early diagnosis has clear implications for overall survival and depends on the liberal use of biopsies of suspicious cutaneous lesions. Proper surgical treatment of the primary tumor (determination of margins of excision) and the decision whether to surgically evaluate the regional nodal basin when it is clinically negative (by sentinel lymph node biopsy) both rely on precise preoperative assessment of primary tumor pathological factors. Accurate measurement of the Breslow thickness, as well as assessment for the presence of ulceration, mitotic rate (especially in thin ≤1 mm melanomas), amongst other primary tumor factors (lymphovascular invasion, satellitosis, regression, Clark’s level), all play a role in the surgical decision-making process. Debate continues regarding the optimal biopsy technique for the diagnosis and initial microstaging of melanoma.
OUTLIERS IN ASSESSMENTS (2008)

ABSTRACT Outliers in assessments are often treated as a nuisance for data analysis; however, they can also assist in quality assurance. Their frequency can suggest problems with form codes, scanning accuracy, ability of examinees to enter responses as they intend, or exposure of items.
A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) in Haloferax volcanii (2014)

The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1-8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.
Estimation of Power System Inertia from Ambient Wide Area Measurements (2019)

This study presents a method of estimating the effective inertia of a power system from ambient frequency and active power signals measured by PMUs. Most importantly, we demonstrate that inertia can be estimated from ambient measurement data, not only from disturbances. This leads to the possibility of monitoring inertia in a close to continuous manner in the time scale of minutes or tens of minutes. The method allows the system to be divided into a number of areas and the effective inertia of each area to be estimated as a separate quantity. In principle, inertia is estimated by observing the dynamics between changes in active power and resulting frequency deviations during normal operation of the system. The method is based on applying system identification on these measurements and extracting inertia values from identified models. Efficacy of the method is demonstrated on results of real measurements from the Icelandic power system.
Detection of mRNA by Reverse Transcription-PCR as an Indicator of Viability in Escherichia coli Cells (1998)

The relationship between the detection of mRNA and cellular viability in Escherichia coli was investigated in cells killed by heat or ethanol. Reverse transcription-PCR (RT-PCR) methods were developed for detecting mRNA from rpoH, groEL, and tufA genes. mRNA from all three genes was detected immediately after the cells had been killed by heat or ethanol but gradually disappeared with time when dead cells were held at room temperature. In heat-killed cells, some mRNA targets became undetectable after 2 to 16 h, whereas after ethanol treatment, mRNA was still detected after 16 h. In contrast, 16S rRNA was detected by RT-PCR in all samples containing dead cells and did not disappear during a subsequent incubation of 16 h at room temperature. Of the different types of nucleic acid, mRNA is the most promising candidate for an indicator of viability in bacteria, but its persistence in dead cells depends on the inactivating treatment and subsequent holding conditions.
A randomized, double-blind, non-inferiority trial evaluating the efficacy and safety of omarigliptin, a once-weekly DPP-4 inhibitor, or glimepiride in patients with type 2 diabetes inadequately controlled on metformin monotherapy (2017)

Objective: To evaluate the efficacy and safety of adding the once-weekly DPP-4 inhibitor omarigliptin or the sulfonylurea glimepiride to the treatment regimen of patients with type 2 diabetes (T2DM) and inadequate glycemic control on metformin monotherapy.Methods: Patients with T2DM and HbA1c ≥6.5% to ≤9.0% while on a stable dose of metformin (≥1500 mg/day) were randomized to omarigliptin 25 mg once-weekly (n = 376) or glimepiride up to 6 mg once daily (n = 375) for 54 weeks. The primary hypothesis was that omarigliptin is non-inferior to glimepiride in reducing HbA1c at week 54.Results: The mean baseline HbA1c was 7.5% in the omarigliptin group and 7.4% in the glimepiride group. After 54 weeks, the least squares (LS) mean change from baseline in HbA1c was –0.30% in the omarigliptin group and –0.48% in the glimepiride group, with a between-group difference (95% CI) of 0.18% (0.06, 0.30), which met the pre-specified criterion for declaring non-inferiority. The incidence of symptomatic hypoglycemia was 5.3% in the omarigliptin group and 26.7% in the glimepiride group. With the exception of hypoglycemia, the incidences of adverse events and discontinuations were similar between treatment groups. Relative to baseline, omarigliptin was associated with a mean weight loss (−0.4 kg) and glimepiride a mean weight gain (+1.5 kg).Conclusions: After 54 weeks, as add-on therapy to metformin, once-weekly omarigliptin was generally well tolerated and non-inferior to glimepiride in improving glycemic control, with a lower incidence of hypoglycemia and with weight loss vs weight gain.
Exploiting cancer cell cycling for selective protection of normal cells. (2001)

Chemotherapy of cancer is limited by its toxicity to normal cells. On the basis of discoveries in signal transduction and cell cycle regulation, novel mechanism-based therapeutics are being developed. Although these cell cycle modulators were designed to target cancer cells, some of them can also be applied for a different purpose, i.e., to protect normal cells against the lethality of chemotherapy. Loss of sensitivity of cancer cells to cell cycle inhibitors can be exploited for selective protection of normal cells that retain this response. Indeed, inhibition of redundant or overactivated pathways (e.g., growth factor-activated pathways) or stimulation of absent pathways in cancer cells (e.g., p53, Rb, and p16) may not arrest cycling of cancer cells. But growth arrest of normal cells will then permit selective killing of cancer cells by cycle-dependent chemotherapy.
Comment on “Peres experiment using photons: No test for hypercomplex (quaternionic) quantum theories” (2017)

In his recent article [Phys. Rev. A 95, 060101(R) (2017)], Adler questions the usefulness of the bound found in our experimental search for genuine effects of hypercomplex quantum mechanics [Nat. Commun. 8, 15044 (2017)]. Our experiment was performed using a black-box (instrumentalist) approach to generalized probabilistic theories; therefore, it does not assume a priori any particular underlying mechanism. From that point of view our experimental results do indeed place meaningful bounds on the possible effects of ``postquantum theories,'' including quaternionic quantum mechanics. In his article, Adler compares our experiment to nonrelativistic and M\"oller formal scattering theories within quaternionic quantum mechanics. With a particular set of assumptions, he finds that quaternionic effects would likely not manifest themselves in general. Although these assumptions are justified in the nonrelativistic case, a proper calculation for relativistic particles is still missing. Here, we provide a concrete relativistic example of Klein-Gordon scattering wherein the quaternionic effects persist. We note that when the Klein-Gordon equation is formulated using a Hamiltonian formalism it displays a so-called ``indefinite metric,'' a characteristic feature of relativistic quantum wave equations. In Adler's example this is directly forbidden by his assumptions, and therefore our present example is not in contradiction to his work. In complex quantum mechanics this problem of an indefinite metric is solved in a second quantization. Unfortunately, there is no known algorithm for canonical field quantization in quaternionic quantum mechanics.
Effects of low concentrations of zinc on the growth and dimorphism of Candida albicans: evidence for zinc-resistant and -sensitive pathways for mycelium formation (1979)

In this analysis we have examined in detail the effects of low concentrations of zinc on the growth and dimorphism of Candida albicans. Evidence is presented that micromolar concentrations of zinc added to growth cultures grown at 25 degrees C (i) cause a twofold increase in the final concentration of spheres at sationary phase, (ii) result in an asynchronous block in the budding cycle at stationary phase, (iii) completely suppress mycelium formation in two independently isolated human strains which produce low but significant levels of mycelia at stationary phase, and (iv) completely suppress mycelium formation in cultures of mutant M10, in which over 60% of the cells form mycelia at stationary phase. In contrast, micromolar concentrations of zinc do not inhibit mycelium formation induced by releasing cells from stationary-phase cultures into fresh medium at 37 degrees C. In addition, if zinc is present in the growth medium of the initial culture at 25 degrees C, the average time of subsequent mycelium formation after release into fresh medium at 37 degrees C is halved. It is demonstrated that the above effects are specific to zinc. The possibility of alterante pathways for mycelium formation is suggested, and the medical implications of this possibility are discussed.
Using the dissipation mode in high resolution atomic force microscopy (2014)

The possibility of using the dissipation mode in high-resolution atomic force microscopy is demonstrated. By the dissipation mode we mean the dynamic mode in which the cantilever oscillates at a resonance frequency and the oscillation amplitude serves as a signal of the feedback tracing a distance to the surface. The possibility of obtaining molecular resolution when scanning in air is shown. The procedure of choosing the optimum scanning parameters is considered.
The Structural Versatility of the BTB Domains of KCTD Proteins and Their Recognition of the GABAB Receptor (2019)

Several recent investigations have demonstrated that members of the KCTD (Potassium Channel Tetramerization Domain) protein family are involved in fundamental processes. However, the paucity of structural data available on these proteins has frequently prevented the definition of their biochemical role(s). Fortunately, this scenario is rapidly changing as, in very recent years, several crystallographic structures have been reported. Although these investigations have provided very important insights into the function of KCTDs, they have also raised some puzzling issues. One is related to the observation that the BTB (broad-complex, tramtrack, and bric-à-brac) domain of these proteins presents a remarkable structural versatility, being able to adopt a variety of oligomeric states. To gain insights into this intriguing aspect, we performed extensive molecular dynamics simulations on several BTB domains of KCTD proteins in different oligomeric states (monomers, dimers, tetramers, and open/close pentamers). These studies indicate that KCTD-BTB domains are stable in the simulation timescales, even in their monomeric forms. Moreover, simulations also show that the dynamic behavior of open pentameric states is strictly related to their functional roles and that different KCTDs may form stable hetero-oligomers. Molecular dynamics (MD) simulations also provided a dynamic view of the complex formed by KCTD16 and the GABA<sub>B2</sub> receptor, whose structure has been recently reported. Finally, simulations carried out on the isolated fragment of the GABA<sub>B2</sub> receptor that binds KCTD16 indicate that it is able to assume the local conformation required for the binding to KCTD.
A comparison of infusion devices at 1 ml/hr. (1993)

Delivery of medications by some infusion devices is irregular. This study investigated instantaneous flow in several infusion devices set at a rate of 1 ml/hr. The following devices were tested: Infusion Pumps: IMED 956A, IVAC 570, IVION "Kids Pump." Syringe Pumps: Medfusion, Baxter, Baxter OR. Tests were performed using a Bio-Tek Infusion Device Analyzer (Model IDA-1). Instantaneous flow rate was defined as Q1/T1 where: Q=sample volume and T=time required to deliver sample volume. The infusion devices were received directly from their respective manufacturers and had not seen clinical service before testing. The units were fully charged and were tested while on AC power. The tests were conducted by the authors, using standard infusion sets and commercially prepared 5% dextrose and 0.45% sodium chloride solution. Each pump was tested for several hours and multiple trials were performed on each pump. The infusion pumps, IMED, IVION, and IVAC all demonstrated deviations from the desired flow rate. The IVAC pump had a greater fluctuation in flow from the set value of 1 ml/hr (p less than 0.02). Variances from mean +/- standard error for each device are shown in parenthesis. IMED 965A (0.005+/-0.014), IVION Kid's Pump (0.002+/-0.009), IVAC 570 (0.001+/-0.006). The Baxter syringe pump (0.002+/-0.009) also had a wide variance in flow. The Baxter OR (0.001+/-0.005) and the Medfusion (0.001+/-0.008) syringe pumps maintained the most consistent flow and showed less variance than the other devices tested.(ABSTRACT TRUNCATED AT 250 WORDS)
Evidence for the synthesis of soluble peptidoglycan fragments by protoplasts of Streptococcus faecalis (1975)

Growing protoplasts of Streptococcus faecalis 9790 were found to synthesize and excrete soluble peptidoglycan fragments. The presence of soluble peptidoglycan derivatives in culture supernatants was determined by (i) incorporation of three different radioactively labeled precursors (L-lysine, D-alanine, and acetate) into products which, after hen egg-white lysozyme hydrolysis, had the same KD values on gel filtration as muramidase hydrolysis products of isolated walls; (ii) inhibition of net synthesis of these products by cycloserine and vancomycin; and (iii) identification of disaccharide-peptide monomer using the beta-elimination reaction, gel filtration, and high-voltage paper electrophoresis. Under the conditions of these experiments the presence of newly synthesized, acid-precipitable (macromolecular) peptidoglycan was not detected. The predominance of monomer (70 to 80%) in lysozyme digests of peptidoglycan synthesized by protoplasts was in sharp contrast to digest of walls from intact streptococci which contain mostly peptide cross-linked products. Biosynthesis and release of relatively uncross-linked, soluble peptidoglycan fragments by protoplasts was related to the absence of suitable, preexisting acceptor wall.
A control system for the optical-fiber piezoelectric modulator of the optical path (2010)

The operating principle of an optical-fiber piezoe lectric modulator of the optical path in all-opti-cal-fiber interferometers is described. The control system of the optical-fiber piezoelectric modulator is composed of a controller based on a field programmable gate array, a digital-to-analog converter, an analog low-pass filter, and a power amplifier. A 4.4-m/s speed of chan ge in the optical length of the fiber has been attained with an error of 0.1% at a modulation length of the optical path of >1 mm.
Animation of Legged Maneuvers: Jumps, Somersaults, and Gait Transitions. (1993)

[in Japanese]
Zur Unmöglichkeit der Geruchsvorhersage (2006)

Abstract Seit mehr als einem Jahrhundert sind Chemiker bestrebt, mehr über die faszinierende und rätselhafte Beziehung zwischen der Molekülstruktur und dem Geruch herauszufinden. Trotz intensiver Forschung zu Struktur‐Geruchs‐Beziehungen bleibt die Vorhersage des Geruchs einer neuen Verbindung aber eine statistische Übung, und Modelle können bestenfalls Aussagen über die Wahrscheinlichkeit von Art, Schwellenwert und Intensität eines Geruchs treffen. Überraschungen sind auf diesem Gebiet alltäglich, und der Zufall bleibt ein wichtiger Faktor bei der Entdeckung neuer Duftstoffe. Neuere Erkenntnisse zum Mechanismus der Geruchswahrnehmung bieten eine Erklärung hierfür und lassen darauf schließen, dass sich unsere Fähigkeit zur Vorhersage der Geruchseigenschaften von Verbindungen in naher Zukunft nicht wesentlich verbessern wird.