Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementary figures and tables

Sascha Dietrich, MD*, Małgorzata Oleś, PhD*, Junyan Lu, PhD*, Leopold Sellner, MD, Simon Anders, PhD, Britta Velten, Bian Wu, MD, Jennifer Hüllein, PhD, Michelle da Silva Liberio, Tatjana Walther, Lena Wagner, Sophie Rabe, Sonja Ghidelli-Disse, Marcus Bantscheff, PhD, Andrzej K. Oleś, PhD, Mikołaj Słabicki, PhD, Andreas Mock, Christopher C. Oakes, PhD, Shihui Wang, Sina Oppermann, Marina Lukas, Vladislav Kim, Martin Sill, PhD, Axel Benner, Anna Jauch, PhD, Lesley Ann Sutton, PhD, Emma Young, Richard Rosenquist, PhD, Xiyang Liu, MD, Alexander Jethwa, Kwang Seok Lee, Joe Lewis, PhD, Kerstin Putzker, Christoph Lutz, MD, Davide Rossi, MD, Andriy Mokhir, PhD, Thomas Oellerich, MD, Katja Zirlik, MD, Marco Herling, MD, Florence Nguyen-Khac, MD, Christoph Plass, PhD, Emma Andersson, Satu Mustjoki, PhD, Christof von Kalle, MD, Anthony D. Ho, MD, Manfred Hensel, MD, Jan Dürig, MD, Ingo Ringshausen, MD, Marc Zapatka, PhD, Wolfgang Huber, PhD and Thorsten Zenz, MD.
FAST-BIST: Faster-than-at-Speed BIST targeting hidden delay defects

Small delay faults may be an indicator of a reliability threat, even if they do not affect the system functionality yet. In recent years, Faster-than-at-Speed-Test (FAST) has become a feasible method to detect faults, which are hidden by the timing slack or by long critical paths in the combinational logic. FAST poses severe challenges to the automatic test equipment with respect to timing, performance, and resolution. In this paper, it is shown how logic built-in self-test (BIST) or embedded deterministic test can be used for an efficient FAST application. Running BIST just at a higher frequency is not an option, as outputs of long paths will receive undefined values due to set time violations and destroy the content of the signature registers. Instead, for a given test pattern sequence, faults are classified according to the optimal detection frequency. For each class, a MISR-based compaction scheme is adapted, such that the critical bits to be observed can be determined by algebraic computations. Experiments show that rather a small number of inter-mediate signatures have to be evaluated to observe a large fraction of hidden delay faults testable by the given test sequence.
The effects of enzyme and inorganic phosphorus supplements in wheat- and rye-based diets on laying hen performance, energy, and phosphorus availability.

A total of 640 22-wk-old pullets (Shaver SX 288) housed four birds per cage in 40 experimental units (four cages per unit), were randomly assigned eight experimental diets in a 2 x 2 x 2 factorial arrangement. The treatments consisting of two grain sources (wheat and rye) two levels each of crude enzyme preparation (0 and 0.1% Roxazyme G), and added inorganic phosphorus (0 and 0.105%) were fed for five 4-wk periods. At 42 wk of age, 40 individually caged layers were fed the experimental diets with 0.3% chromic oxide (5 individual birds per treatment) to determine AMEn and available P. Plasma P and Ca were also determined. Egg production, feed intake (FI), egg weight, feed efficiency (FE), and specific gravity of eggs were significantly (P < or = 0.05) affected by the experimental periods. Hens fed wheat-based diets had higher (P < or = 0.05) tibia ash (54.3 vs 52.5%), excreta dry matter (22.0 vs 17.7%), and eggshells with > or = 1.080 specific gravity (93.5 vs 89.9%) than birds fed rye. Enzyme supplementation significantly improved AMEn (P < or = 0.01) and FE by 6.2 and 3%, respectively. Egg production increased numerically from 87.6 to 90.1%. Inorganic P supplementation significantly increased egg production (P < or = 0.01), FI, FE, and AMEn (P < or = 0.05) by 4.4, 2, 3, and 2.8%, respectively, but significantly (P < or = 0.05) decreased the proportion of eggs having a specific gravity > or = 1.080 from 92.8 to 90.6%. The enzyme and inorganic P supplementation had no effect on tibia ash content and total plasma Ca and P. Rye can be used in layer rations yielding satisfactory performance when fed with a fungal crude enzyme preparation high in pentosanase/xylanase activity.
Super-resolution binding activated localization microscopy through reversible change of DNA conformation

ABSTRACT Methods of super-resolving light microscopy (SRM) have found an exponentially growing range of applications in cell biology, including nuclear structure analyses. Recent developments have proven that Single Molecule Localization Microscopy (SMLM), a type of SRM, is particularly useful for enhanced spatial analysis of the cell nucleus due to its highest resolving capability combined with very specific fluorescent labeling. In this commentary we offer a brief review of the latest methodological development in the field of SMLM of chromatin designated DNA Structure Fluctuation Assisted Binding Activated Localization Microscopy (abbreviated as fBALM) as well as its potential future applications in biology and medicine.
Validity and reliability of smartphone orientation measurement to quantify dynamic balance function

Objective: Postural control is frequently compromised after sub-concussive and concussive head trauma, and balance testing is an integral part of neuromotor assessment and management. The main objective of this paper is to develop a novel smartphone-based neuromotor assessment protocol for screening of dynamic balance decrements stemming from head trauma. Approach: Experiments 1 and 2 compared Android smartphone orientation detection algorithms to a biomechanics laboratory motion capture system using a pendulum (i.e. non-biological movement) and a human stepping task (i.e. biological movement). Experiment 3 examined the test-retest reliability of a stepping-in-place protocol in three different sensory conditions (eyes open, no-vision, head shake) using temporal and spatial variability metrics extracted from thigh orientation signal in a sample of healthy young adults. Main results: Smartphone sensors provided valid measurements of movement timing and amplitude variables. However, sensor firmware version and Android OS version significantly affected quality of measurement. High test-retest reliability was shown for the temporal and spatial variables of interest during the stepping-in-place task. Significance: Collectively, these experiments show that our smartphone application is a valid and reliable way to measure leg movement characteristics (mean stride time and its variability (CV), Peak Thigh SD, Thigh ROM, and Peak Return Velocity) during dynamic balance activity, which could provide an objective way to assess neuromotor function after head trauma and in other populations with balance dysfunction.
Research note: variability in preincubation embryonic development in domestic fowl. 2. Effects of duration of egg storage period.

Embryos of eggs from Single Comb White Leghorn hens were analyzed to determine whether duration of egg storage significantly affects embryonic development prior to incubation. Eggs were gathered over a period of 5 days from 25-wk-old hens that were naturally inseminated and housed in floor pens. Within 1 h of oviposition the eggs were collected and assigned randomly to one of five storage treatment groups of 0, 4, 7, 14, or 21 days. Fresh egg weight was recorded and the eggs were placed on plastic egg flats and stored at 14 C. Weight of each egg was measured after storage to determine amount of weight lost during storage. A total of 500 embryos were examined after storage. Viable embryos were staged for development using a modified Eyal-Giladi and Kochav classification. The incidence of embryonic mortality was noted. Duration of storage (P = .5815) collection date (P = .5815), and fresh egg weight (P = .3789) did not affect embryonic development significantly. A significant linear relationship was observed between duration of the storage period and loss of egg weight (P = .0001). Embryonic mortality was significantly related to loss of egg weight (P = .0001). Mortality was highest in eggs that were stored for a longer period of time. The data from the current study indicate that storing fertile eggs below physiological zero inhibits embryonic development. One of the reasons for the increased incidence of embryonic mortality in eggs that were stored for longer periods may be related to the increased egg weight loss in these eggs.
Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata*

Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine.
A universal-algebraic proof of the complexity dichotomy for Monotone Monadic SNP

The logic MMSNP is a restricted fragment of existential second-order logic which allows to express many interesting queries in graph theory and finite model theory. The logic was introduced by Feder and Vardi who showed that every MMSNP sentence is computationally equivalent to a finite-domain constraint satisfaction problem (CSP); the involved probabilistic reductions were derandomized by Kun using explicit constructions of expander structures. We present a new proof of the reduction to finite-domain CSPs that does not rely on the results of Kun. This new proof allows us to obtain a stronger statement and to verify the Bodirsky-Pinsker dichotomy conjecture for CSPs in MMSNP. Our approach uses the fact that every MMSNP sentence describes a finite union of CSPs for countably infinite ω-categorical structures; moreover, by a recent result of Hubička and Nešetřil, these structures can be expanded to homogeneous structures with finite relational signature and the Ramsey property. This allows us to use the universal-algebraic approach to study the computational complexity of MMSNP.
A Forest Transect of Pine Mountain , Kentucky : Changes Since

In 1997, forest composition and structure were determined for Hi Lewis Pine Barrens State Nature Preserve, a 68-ha tract on the south slope of Pine Mountain, Harlan County, Kentucky. Data collected from 28 0.04-ha plots were used to delineate forest types. Percent canopy compositions were compared with those reported by Dr. E. Lucy Braun prior to the peak of chestnut blight. Four forest types were identified: Liriodendron-Acer, Quercus-Tsuga, Mixed Quercus, and Pinus-Quercus. Post-blight, little change has occurred in the Pinus-Quercus forest type on ridges and SSE aspects. On more mesic aspects, canopy gaps created by chestnut death were filled primarily by existing canopy species (Quercus spp.) and to a lesser degree by non-canopy species. Near the crest of the mountain, Acer rubrum has replaced Castanea dentata and assumed secondary importance to Liriodendron tulipifera. Castanea dentata remains an important component in the subcanopy of the four forest types and is present in the groundcover in three types. Except for the absence of C. dentata, species composition of Braun’s forest types has remained relatively unchanged during the past 70 years; however, loss of C. dentata initiated changes in the relative importance of these species resulting in varying degrees of transition to post-blight forest types. Contribution of existing canopy species to importance values for the subcanopy and woody groundcover strata is less than that of fire-sensitive species, suggesting future changes in these post-blight forest communities.
Distinct spatiotemporal patterns of neuronal functional connectivity in primary progressive aphasia variants

Primary progressive aphasia is a syndrome characterized by progressive loss of language abilities with three main phenotypic clinical presentations, including logopenic, non-fluent/agrammatic, and semantic variants. Previous imaging studies have shown unique anatomic impacts within language networks in each variant. However, direct measures of spontaneous neuronal activity and functional integrity of these impacted neural networks in primary progressive aphasia are lacking. The aim of this study was to characterize the spatial and temporal patterns of resting state neuronal synchronizations in primary progressive aphasia syndromes. We hypothesized that resting state brain oscillations will show unique deficits within language network in each variant of primary progressive aphasia. We examined 39 patients with primary progressive aphasia including logopenic variant (n = 14, age = 61 ± 9 years), non-fluent/agrammatic variant (n = 12, age = 71 ± 8 years) and semantic variant (n = 13, age = 65 ± 7 years) using magnetoencephalographic imaging, compared to a control group that was matched in age and gender to each primary progressive aphasia subgroup (n = 20, age = 65 ± 5 years). Each patient underwent a complete clinical evaluation including a comprehensive battery of language tests. We examined the whole-brain resting state functional connectivity as measured by imaginary coherence in each patient group compared to the control cohort, in three frequency oscillation bands-delta-theta (2-8 Hz); alpha (8-12 Hz); beta (12-30 Hz). Each variant showed a distinct spatiotemporal pattern of altered functional connectivity compared to age-matched controls. Specifically, we found significant hyposynchrony of alpha and beta frequency within the left posterior temporal and occipital cortices in patients with the logopenic variant, within the left inferior frontal cortex in patients with the non-fluent/agrammatic variant, and within the left temporo-parietal junction in patients with the semantic variant. Patients with logopenic variant primary progressive aphasia also showed significant hypersynchrony of delta-theta frequency within bilateral medial frontal and posterior parietal cortices. Furthermore, region of interest-based analyses comparing the spatiotemporal patterns of variant-specific regions of interest identified in comparison to age-matched controls showed significant differences between primary progressive aphasia variants themselves. We also found distinct patterns of regional spectral power changes in each primary progressive aphasia variant, compared to age-matched controls. Our results demonstrate neurophysiological signatures of network-specific neuronal dysfunction in primary progressive aphasia variants. The unique spatiotemporal patterns of neuronal synchrony signify diverse neurophysiological disruptions and pathological underpinnings of the language network in each variant.
Log-linear model-based multifactor dimensionality reduction method to detect gene-gene interactions

MOTIVATION The identification and characterization of susceptibility genes that influence the risk of common and complex diseases remains a statistical and computational challenge in genetic association studies. This is partly because the effect of any single genetic variant for a common and complex disease may be dependent on other genetic variants (gene-gene interaction) and environmental factors (gene-environment interaction). To address this problem, the multifactor dimensionality reduction (MDR) method has been proposed by Ritchie et al. to detect gene-gene interactions or gene-environment interactions. The MDR method identifies polymorphism combinations associated with the common and complex multifactorial diseases by collapsing high-dimensional genetic factors into a single dimension. That is, the MDR method classifies the combination of multilocus genotypes into high-risk and low-risk groups based on a comparison of the ratios of the numbers of cases and controls. When a high-order interaction model is considered with multi-dimensional factors, however, there may be many sparse or empty cells in the contingency tables. The MDR method cannot classify an empty cell as high risk or low risk and leaves it as undetermined. RESULTS In this article, we propose the log-linear model-based multifactor dimensionality reduction (LM MDR) method to improve the MDR in classifying sparse or empty cells. The LM MDR method estimates frequencies for empty cells from a parsimonious log-linear model so that they can be assigned to high-and low-risk groups. In addition, LM MDR includes MDR as a special case when the saturated log-linear model is fitted. Simulation studies show that the LM MDR method has greater power and smaller error rates than the MDR method. The LM MDR method is also compared with the MDR method using as an example sporadic Alzheimer's disease.
The effect of feeding various levels of lead on the performancef broilers.

Abstract Most commercial sources of zinc contain varying amounts of lead, and the manufacturers of trace mineral mixes have been concerned about keeping the lead levels as low as possible in their finished product. Lead poisoning of waterfowl and migratory birds appears to result from the ingestion of spent lead shot, and studies have been conducted to determine the severity and elucidate the symptoms of this malady (Lewis and Legler, 1968; Bagley et al., 1967). Grandy et al. (1968) investigated the relative toxicity of lead and several other proposed substitute shot types to 18-month-old Mallard drakes. All of the birds dosed with commercial lead (eight number 6 shot) died within 15 days. Two other shot types, a tin-lead alloy and zinc, resulted in mortality rates of 27 and 20%, respectively. There were no deaths among ducks dosed with nickel, teflon-coated steel, or tin. A report by Cook and Trainer (1966) indicated…
Chronic stimulant use: An upcoming cause of neurocognitive disorder in later life?

Objective: Alert for chronic stimulant use as an etiological factor of a major neurocognitive disorder. Methods: Single-case study. Results: A 58-year-old woman, with a history of chronic daily stimulant use, was diagnosed with a major neurocognitive disorder with behavioral problems. Conclusion: This case highlights the possibility of chronic daily stimulant use resulting in a major neurocognitive disorder. Since the prevalence of long-lasting illicit stimulant use among older adults is rising, we suggest considering this as a possible etiological factor of neurocognitive disorders.
Radiomic biomarkers from PET/CT multi-modality fusion images for the prediction of immunotherapy response in advanced non-small cell lung cancer patients

Purpose: Investigate the ability of using complementary information provided by the fusion of PET/CT images to predict immunotherapy response in non-small cell lung cancer (NSCLC) patients. Materials and methods: We collected 64 patients diagnosed with primary NSCLC treated with anti PD-1 checkpoint blockade. Using PET/CT images, fused images were created following multiple methodologies, resulting in up to 7 different images for the tumor region. Quantitative image features were extracted from the primary image (PET/CT) and the fused images, which included 195 from primary images and 1235 features from the fusion images. Three clinical characteristics were also analyzed. We then used support vector machine (SVM) classification models to identify discriminant features that predict immunotherapy response at baseline. Results: A SVM built with 87 fusion features and 13 primary PET/CT features on validation dataset had an accuracy and area under the ROC curve (AUROC) of 87.5% and 0.82, respectively, compared to a model built with 113 original PET/CT features on validation dataset 78.12% and 0.68. Conclusion: The fusion features shows better ability to predict immunotherapy response prediction compared to individual image features.
Predictive Movements and Human Reinforcement Learning of Sequential Action

Abstract Sequential action makes up the bulk of human daily activity, and yet much remains unknown about how people learn such actions. In one motor learning paradigm, the serial reaction time (SRT) task, people are taught a consistent sequence of button presses by cueing them with the next target response. However, the SRT task only records keypress response times to a cued target, and thus it cannot reveal the full time‐course of motion, including predictive movements. This paper describes a mouse movement trajectory SRT task in which the cursor must be moved to a cued location. We replicated keypress SRT results, but also found that predictive movement—before the next cue appears—increased during the experiment. Moreover, trajectory analyses revealed that people developed a centering strategy under uncertainty. In a second experiment, we made prediction explicit, no longer cueing targets. Thus, participants had to explore the response alternatives and learn via reinforcement, receiving rewards and penalties for correct and incorrect actions, respectively. Participants were not told whether the sequence of stimuli was deterministic, nor if it would repeat, nor how long it was. Given the difficulty of the task, it is unsurprising that some learners performed poorly. However, many learners performed remarkably well, and some acquired the full 10‐item sequence within 10 repetitions. Comparing the high‐ and low‐performers’ detailed results in this reinforcement learning (RL) task with the first experiment's cued trajectory SRT task, we found similarities between the two tasks, suggesting that the effects in Experiment 1 are due to predictive, rather than reactive processes. Finally, we found that two standard model‐free reinforcement learning models fit the high‐performing participants, while the four low‐performing participants provide better fit with a simple negative recency bias model.