gebhart/patrepeval huggingface dataset:
Group testing with DNA chips: generating designs and decoding experiments (2004)

DNA microarrays are a valuable tool for massively parallel DNA-DNA hybridization experiments. Currently, most applications rely on the existence of sequence-specific oligonucleotide probes. In large families of closely related target sequences, such as different virus subtypes, the high degree of similarity often makes it impossible to find a unique probe for every target. Fortunately, this is unnecessary. We propose a microarray design methodology based on a group testing approach. While probes might bind to multiple targets simultaneously, a properly chosen probe set can still unambiguously distinguish the presence of one target set from the presence of a different target set. Our method is the first one that explicitly takes cross-hybridization and experimental errors into account while accommodating several targets. The approach consists of three steps: (1) Pre-selection of probe candidates, (2) Generation of a suitable group testing design, and (3) Decoding of hybridization results to infer presence or absence of individual targets. Our results show that this approach is very promising, even for challenging data sets and experimental error rates of up to 5%. On a data set of 28S rDNA sequences we were able to identify 660 sequences, a substantial improvement over a prior approach using unique probes which only identified 408 sequences.
Silicon LEDs fabricated in standard VLSI technology as components for all silicon monolithic integrated optoelectronic systems (2002)

It is shown that, by using conventional VLSI design rules and device processing, a variety of two terminal and multiterminal integrated silicon light-emitting devices (Si-LEDs) can be routinely fabricated without any adaptation to the process, enabling the production of all-silicon monolithic optoelectronic systems. Their specific performance can be tailored by their different geometries and structures, yielding, by design, area, line, and point light-emitting patterns. The light-generating mechanisms are based on carrier quantum transitions in Si pn junctions, operated in the field emission or avalanche modes. Field emission Si-LEDs can operate at supply voltages compatible with those of integrated circuits (5 V or less). Avalanche Si-LEDs require higher operating voltages, but yield higher light intensities. The two terminal Si-LEDs yield a linear relation between the emitted light intensity and the driving current. The multiterminal Si-LEDs exhibit a nonlinear relation between the light emission intensity and the controlling electrical signal, enabling signal processing operations, which can not be attained in two terminal Si-LEDs. Two basic structures of multi terminal Si-LEDs are presented, i.e MOS-like structures, or carrier injection based structures (BJT-like devices). They possess different input impedances and both their emitted light intensities and emitting area patterns can be controlled by the input electrical signal.
Bra strap orientations and designs to minimise bra strap discomfort and pressure during sport and exercise in women with large breasts (2015)

Bra straps that are vertically orientated and wide (approximately 4.5 cm in width) are preferable for women with large breasts during sport and exercise to minimise bra strap pressure and discomfort. The addition of gel pads under bra straps may also decrease discomfort and prevent straps slipping off the shoulders, although this notion warrants further investigation.
Nonlinear Interaction Imaging and Spectroscopy in Scanning Probe Microscopy (2010)

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
Performance of commercial broilers under different intermittant lighting programs (2015)

An experiment was conducted to study the effect of intermittent lighting program on the performance and carcass yield of commercial broilers. The light treatment from 14 days onwards up to 42 days was given as 23 hr light and 1 hr darkness for continuous light program and 4 hr light and 2 hr darkness intermittently for intermittent light program. The results indicated that there was no significant difference in body weight at 14, 35 and 42 days of age in both treatments. Continuous lighting produced significantly higher body weight at 21 and 28 days of age. Feed conversion efficiency (FCR) did not differ significantly at 14, 21, and 28 days of age. But it was significantly better in intermittent lighting regime after 35 days of age. Carcass yield and drumstick were significantly higher for intermittent lighting treatment. Continuous light treatment produced significantly higher fillets and tenders at 42 days of age.
Deep Brain Stimulation of the Lateral Habenular Complex in Treatment-Resistant Depression (2012)

Targeting LHb-c is a feasible and safe technique in the majority of patients undergoing surgery for DBS. However, meticulous individual planning to avoid interference with ventricles and thalamus-related veins is mandatory because an alternative steep frontal entry point has to be considered in about half of the patients.
Multidirectional flexibility analysis of cervical artificial disc reconstruction: in vitro human cadaveric spine model (2005)

The stand-alone cervical 3D FD demonstrated nearly physiological biomechanical characteristics at both operative and adjacent spinal segments in vitro, indicating an excellent clinical potential for cervical artificial disc replacement.
Effect of pain scrambler therapy on shoulder joint pain and range of motion in patients who had undergone arthroscopic rotator cuff repair for the first time (2016)

[Purpose] This study aimed to determine the effect of pain scrambler therapy on shoulder joint pain and range of motion in patients who had undergone arthroscopic rotator cuff repair for the first time. [Subjects and Methods] Pain scrambler therapy was administered once a day every 40 minutes for 10 days to patients that had undergone arthroscopic rotator cuff repair for the first time. The visual analog scale was used to measure pain, and a goniometer was used to measure shoulder range of motion. [Results] After 10 sessions of pain scrambler therapy, pain was significantly reduced from that before the treatment. In addition, shoulder range of motion was increased after 10 treatment sessions. [Conclusion] Thus, pain scrambler therapy greatly reduced pain and increased should range of motion in the patients who had undergone arthroscopic rotator cuff repair for the first time.
Incidence of Aflatoxin in California Almonds (1975)

In a survey of California almonds, aflatoxin was found in 14% of 74 samples of unsorted, in-shell almonds as received by the processor in 1972, but it occurred at very low levels (below 20 parts per billion (ppb)) in 90% of the contaminated samples. The overall proportion of individual nuts contaminated was especially low and is estimated with 95% probability to have been in the range of 1 nut/55,300 nuts to 1 nut/14,700 nuts. Aflatoxin contamination is not restriced to any particular section of the almond-growing region of California. Commercial sorting procedures are effective in removing most aflatoxin-contaminated nutmeats, since none of 26 samples of processed, whole nutmeats contained aflatoxin. In contrast, 13 of 27 samples of diced almonds were contaminated, but nine of these 13 samples contained less than 20 ppb. Only one of 25 samples of sliced nutmeats contained aflatoxin (4 ppb). Thus, aflatoxin incidence in almonds varies greatly with the category of finished product. The apparent high incidence in diced nutmeats is probably due mostly to the more uniform distribution of aflatoxin occurring in this product (because of its small particle size) than that occurring in the other products. Sample size requirements for monitoring aflatoxin in almonds are discussed.
Integrated temporal and spatial scheduling for extended operand clustered VLIW processors (2004)

Centralized register file architectures scale poorly in terms of clock rate, chip area, and power consumption and are thus not suitable for consumer electronic devices. The consequence is the emergence of architectures having many interconnected clusters each with a separate register file and a few functional units. Among the many inter-cluster communication models proposed, the extended operand model extends some of operand fields of instruction with a cluster specifier and allows an instruction to read some of the operands from other clusters without any extra cost.Scheduling for clustered processors involves spatial concerns (where to schedule) as well as temporal concerns (when to schedule). A scheduler is responsible for resolving the conflicting requirements of aggressively exploiting the parallelism offered by hardware and limiting the communication among clusters to available slots. This paper proposes an integrated spatial and temporal scheduling algorithm for extended operand clustered VLIW processors and evaluates its effectiveness in improving the run time performance of the code without code size penalty.
A 10-GHz CMOS LC VCO with Wide Tuning Range Using Capacitive Degeneration (2006)

Abstract—In order to widen the tuning range, capacitive degeneration is applied to fully CMOS LC VCOs. Small signal analysis shows that the fixed MOSFET capacitance seen by the LC tank is smaller than that of the traditional LC VCO, resulting in significant extension in the tuning range. This improvement in the tuning range has been verified through measurement of a 10-GHz LC VCO fabricated by 0.18 ㎛ CMOS process. The measured tuning range is from 9.8-GHz to 12-GHz, which is better than those of the reported CMOS LC VCOs in 10-GHz band. The measured phase noise is-103dBc/Hz at 1MHz offset. Index Terms—capacitive degeneration, parasitic capacitance, tuning range, voltage-controlled oscillator(VCO). I.
Invisibility cloaking based on geometrical optics for visible light (2013)

Optical cloaking has been one of unattainable dreams and just a subject in fiction until recently. Several different approaches to cloaking have been proposed and demonstrated: stealth technology, active camouflage and transformation optics. The last one would be the most formal approach modifying electromagnetic field around an object to be cloaked with metamaterials. While cloaking based on transformation optics, though valid only at single frequency, is experimentally demonstrated in microwave region, its operation in visible spectrum is still distant from realisation mainly owing to difficulty in fabricating metamaterial structure whose elements are much smaller than wavelength of light. Here we show that achromatic optical cloaking in visible spectrum is possible with the mere principle based on geometrical optics. In combining a pair of polarising beam splitters and right-angled prisms, rays of light to be obstructed by an object can make a detour to an observer, while unobstructed rays go straight through two polarising beam splitters. What is observed eventually through the device is simply background image as if nothing exists in between.
Applications of context-aware computing in hospital work (2004)

Context-awareness is a key concept in ubiquitous computing, which sometimes seems to be a technology looking for a purpose. In this paper we report on the application of context-aware computing for medical work in hospitals, which has appeared to be a strong case for applying context-aware computing. We present the design of a context-aware pill container and a context-aware hospital bed, both of which reacts and adapts according to what is happening in their context. The applications have been evaluated in a number of workshop with clinicians and patients. Based on this empirical work of designing, developing, and evaluating context-aware clinical applications, the paper outlines some key design principles for a context-awareness framework, supporting the development and deployment of context-aware clinical computer applications.
Improving locality and parallelism in nested loops (1992)

Researchers have identified a core set of program transformations that are effective in array-based loop nest optimization: these loop transformations include interchange, skewing, reversal and tiling. Researchers have studied these transformations individually for their legality and effect on parallelism and memory hierarchy performance; but they have not discussed in any detail how to choose the combination of transformations that best optimizes a loop nest. Other researchers have taken another approach: they consider each loop nest as a whole, applying an elegant matrix theory of loop nest transformation, but one that is only applicable to a limited class of loop nests, those whose dependences can be expressed as distance vectors. In this limited context, the problems of memory hierarchy improvement and parallelization are simplified, but their approach has not been extended to apply to general loop nests.
We have combined the elegance of the matrix theory with the generality of general dependence vectors into a new theory of loop transformation. This theory has enabled us to apply an algorithmic approach to solving optimization goals. Using this theory, we have developed efficient algorithms for the compiler to use to improve memory hierarchy utilization and parallelism of general loop nests. The parallelization improving algorithm maximizes the degree of parallelism within a loop nest, at either a coarse or fine granularity. The locality improving algorithm uses the same theory, and also reuse information about array accesses within loop nests, to guide the transformation process. The parallelization and locality improvement algorithms are unified so that locality and parallelism can be improved simultaneously without significantly reducing either.
We have implemented versions of these algorithms in Stanford's SUIF compiler and performed experimentation on the Perfect Club and the NASA kernels. We have found compiler locality improvement to significantly improve performance when applicable. We have also demonstrated a tremendous sensitivity of performance on tile size for tiled codes on machines with direct-mapped or low set associativity caches.
Kinetics of Eucalypt Lignosulfonate Oxidation to Aromatic Aldehydes by Oxygen in Alkaline Medium (2010)

The oxidation kinetics of lignosulfonates (LS) from acidic magnesium-based sulfite pulping of Eucalyptus globulus wood with oxygen under alkaline conditions was studied. The analysis of oxidation products in the reaction system O2/NaOH revealed a predominance of aromatic aldehydes (vanillin and syringic aldehyde) though small amounts of vanillic and syringic acids and acetophenone/phenylacetaldehyde derivatives have also been detected. The rate constant of syringic aldehyde formation was roughly twice of that for vanillin. The effective activation energies for the oxidation of LS to aromatic aldehydes (ca. 60−70 kJ/mol) were rather different to those found for the formation of aromatic acids (ca. 110 kJ/mol) indicating different mechanisms involved in the rate-determining reaction step. The addition of catalyst (copper salt, 20% w/w) promoted the LS oxidation with increments of aromatic aldehyde yields by 25−50%. The maximum yields of syringic aldehyde and vanillin upon LS oxidation were 16.1 and 4.5%, respectively (150 °C, 20 min, PO2 = 10 bar, 0.9 M NaOH solution). The highly negative effect of concomitant sugars in sulfite liquor to the yield of aromatic aldehydes was highlighted.
Brain Output Dysregulation Induced by Olfactory Bulbectomy: An Approximation in the Rat of Major Depressive Disorder in Humans? (1988)

Mounting evidence indicates that the emotional, cognitive, neurovegetative and behavioral symptoms of patients with major depressive disorder are due to abnormal neurochemical substrates in the brain. Although the specific neurochemical abnormalities responsible have not been identified, the presenting symptoms of major depression are consistent with a disruption of normal neural communications between the limbic system and hypothalamus. Following removal of the olfactory bulbs, rats display a syndrome of behavioral deficits that also reflect a disruption of the limbic-hypothalamic axis. Moreover, the bulbectomy induced deficits are selectively reduced by the chronic administration of the same drugs that alleviate the symptoms of depression when given chronically to the patients. In addition to this pharmacological similarity, there are also numerous behavioral parallels between bulbectomized rats and major depression patients. The bulbectomized rat provides a good model in which to study antidepressant drugs and also may provide neurochemical and neuroanatomical data that are relevant to understanding the biological substrates of emotion and the causes of depression in humans.
Carcinogenicity of formaldehyde in rats and mice after long-term inhalation exposure. (1983)

Groups of approximately 120 male and 120 female Fischer 344 rats and C57BL/6 X C3H F1 mice were exposed by inhalation to 0, 2.0, 5.6, and 14.3 ppm of formaldehyde gas 6 hr/day, 5 days/week, for 24 months. This exposure period was followed by up to 6 months of nonexposure. Interim sacrifices were conducted at 6, 12, 18, 24, 27, and 30 months. Significant formaldehyde-induced lesions were restricted to the nasal cavity and proximal trachea. The distribution and severity of these lesions were concentration dependent. Rhinitis, epithelial dysplasia, and squamous metaplasia occurred in all exposure groups of rats and in the intermediate and high exposure groups of mice. There was regression of rhinitis, dysplasia, and metaplasia at 27 months (3 months postexposure) in the 14.3- and 5.6-ppm groups of mice and in the 2.0- and 5.6-ppm groups of rats. Squamous cell carcinomas were observed in the nasal cavities of 103 rats (52 females and 51 males) and 2 male mice exposed to 14.3 ppm and in 2 rats (one male and one female) exposed to 5.6 ppm of formaldehyde gas. Formaldehyde inhalation was also weakly associated with an increase in the frequency of polypoid adenomas in the nasal cavity of male rats.
Continuous cell lines with altered growth and differentiation properties originate after transfection of human keratinocytes with human papillomavirus type 16 DNA (1988)

Immortalization of human keratinocytes (HKc) by human papillomavirus type 16 (HPV16) is reproducible at a high frequency, is due directly to the presence of the viral sequences in the cells, and occurs independently from the genetic characteristics of the host cells. Ten human keratinocyte strains, each derived from a different individual, were transfected with pMHPV16d and selected with G418. Eight became established lines. Two strains, which failed to grow shortly after successful G418 selection, were negative for HPV16 DNA. No lines were established following transfection of the same HKc strains with vector sequences only. The immortalized lines maintained a constant number of copies of the viral genome integrated into the cellular DNA. Each line showed a unique integration pattern of HPV16 sequences into the cellular genome, but expressed similar patterns of viral messages. Sublines able to grow in the absence of growth factors (epidermal growth factor and bovine pituitary extract), and others which became resistant to differentiation stimuli (serum and calcium) were obtained by selection in growth factor-free medium and serum-supplemented medium, respectively. The establishment of continuous cell lines is a direct consequence of the presence of viral sequences; however, because none of these lines formed tumors in nude mice, additional events must be necessary for progression of malignancy. HPV16-immortalized human keratinocyte lines can be used to investigate and identify the viral factors involved with the modification of growth and differentiation control by HPV16.
Design and first results of CytoBuoy: A wireless flow cytometer for in situ analysis of marine and fresh waters (1999)

CytoBuoy allows on-line in situ particle analysis, estimation of phytoplankton biomass, and discrimination between different phytoplankton groups. This will increase the applicability of flow cytometry in the field of environmental monitoring.
Solution-processed organic transistors based on semiconducting blends (2010)

The latest advances in the use of solution processable organic semiconductor blends for organic field effect transistor (OFET) applications are reviewed. We summarise multi-component, thin film microstructure formation from solution with particular focus on phase separation and crystallisation of components. These approaches can then be applied to semiconducting materials and their use in organic devices. Several key applications are studied, namely ambipolar systems with n- and p-type components, high charge carrier mobility and uniform films for high performance OFETs, and the potential for self-assembly during OFET fabrication. Blending materials can in all cases be used to combine the advantageous properties of the individual components.
Robust Federated Learning: The Case of Affine Distribution Shifts (2020)

Federated learning is a distributed paradigm that aims at training models using samples distributed across multiple users in a network while keeping the samples on users' devices with the aim of efficiency and protecting users privacy. In such settings, the training data is often statistically heterogeneous and manifests various distribution shifts across users, which degrades the performance of the learnt model. The primary goal of this paper is to develop a robust federated learning algorithm that achieves satisfactory performance against distribution shifts in users' samples. To achieve this goal, we first consider a structured affine distribution shift in users' data that captures the device-dependent data heterogeneity in federated settings. This perturbation model is applicable to various federated learning problems such as image classification where the images undergo device-dependent imperfections, e.g. different intensity, contrast, and brightness. To address affine distribution shifts across users, we propose a Federated Learning framework Robust to Affine distribution shifts (FLRA) that is provably robust against affine Wasserstein shifts to the distribution of observed samples. To solve the FLRA's distributed minimax problem, we propose a fast and efficient optimization method and provide convergence guarantees via a gradient Descent Ascent (GDA) method. We further prove generalization error bounds for the learnt classifier to show proper generalization from empirical distribution of samples to the true underlying distribution. We perform several numerical experiments to empirically support FLRA. We show that an affine distribution shift indeed suffices to significantly decrease the performance of the learnt classifier in a new test user, and our proposed algorithm achieves a significant gain in comparison to standard federated learning and adversarial training methods.
Sneeze related area in the medulla: localisation of the human sneezing centre? (2005)

Sneezing is a rarely explored symptom in neurological practice. In the cat, a sneeze evoking centre is located in the medulla. The existence of a sneezing centre has not been confirmed in humans. A case with abnormal sneezing secondary to a strategic infarct in the right latero-medullary region is presented. A 66 year old man suddenly presented paroxysmal sneezing followed by ataxia, right sided motor and sensory symptoms, and hoarseness. The application of stimuli to the right nasal fossa did not evoke sneezing nor the wish to sneeze. The same stimuli to the contralateral nasal fossa evoked normal sneezing. The preservation of the superficial sensitivity of the nasal fossa indicates that the lesion was localised in the hypothetical human sneezing centre, very close to the spinal trigeminal tract and nucleus. This centre appears to be bilateral and functionally independent on both sides.