Miracle-dz/UniFAR-FTUs huggingface dataset:
Supplementary Figures

Supplementary Figure 1 | STM/AFM Observation of H2O/Cu(110) with CO-terminal tips. a, STM image of Cu(110) after depositing water at 78 K and CO at 8 K (V = 30 mV, I = 20 pA). The image was obtained at 4.8 K with a Cu-terminal tip. b, STM image of the same area as in a but obtained with a CO-terminal tip. c, The same images as in Fig. 1d in the main text but without the schematic model. d–f, The same STM, AFM, and Laplacian-filtered AFM images as in Fig. 2j, k, and l in the main text, respectively, but with the yellow lines representing the lattice of surface Cu atoms (the unit cell is 2.56
Combining discriminative features to infer complex trajectories

We propose a new model for the probabilistic estimation of continuous state variables from a sequence of observations, such as tracking the position of an object in video. This mapping is modeled as a product of dynamics experts (features relating the state at adjacent time-steps) and observation experts (features relating the state to the image sequence). Individual features are flexible in that they can switch on or off at each time-step depending on their inferred relevance (or on additional side information), and discriminative in that they need not model the full generative likelihood of the data. When trained conditionally, this permits the inclusion of a broad range of rich features (for example, features relying on observations from multiple time-steps), and allows the relevance of features to be learned from labeled sequences.
Peripheral Anterior Synechiae and Ultrasound Biomicroscopic Parameters in Angle-Closure Glaucoma Suspects

Purpose To investigate the correlation between peripheral anterior synechia (PAS) and the quantitative anterior chamber angle parameters measured by ultrasound microscopy (UBM) in angle-closure glaucoma suspect (ACGS) eyes. Methods Eyes were defined ACGS as having occludable angles and intraocular pressure less than 21 mm Hg without glaucomatous optic nerve head. The gonioscopic criteria for ACGS were the trabecular meshwork invisible in 3 or more quadrants of the entire angle and the angular width less than 20 degrees by Shaffer classification. Twenty-seven eyes of 20 patients underwent anterior chamber angle and ciliary body imaging with UBM. Angle opening distance (AOD500), angle recess area (ARA), trabecular-ciliary process distance (TCPD) and trabecular-iris angle (TIA) were measured from the UBM images at each quadrant. Results The AOD500, ARA, and TIA were not significantly different between the eyes with PAS (9 eyes)and without PAS (18 eyes) at each quadrant. However, the TCPD was significantly shorter in the superior quadrant when compared with the eyes without PAS (mean: 405.3±70.9 µm vs 536.4±140.5 µm) (p<0.05). Conclusions The results suggest that the shorter distance from trabecular meshwork to ciliary body or the anterior placement of ciliary process may play a role in the development of PAS in ACGS eyes.
Amitriptyline and methylphenidate treatment of behaviorally disordered children.

SUMMARY A controlled investigation was conducted to assess the relative effectiveness of amitriptyline and methylphenidate for treating hyperactive/aggressive behavior in children originally referred to a learning clinic. Behavioral change was measured through parent and teacher ratings. Drug effects on attention, short term memory, and impulsivity were evaluated with laboratory tasks. It was found that both drugs were largely comparable in attenuating hyperactivity and aggression. Of the laboratory measures, only attention was improved by both drugs. However, neither medication interfered with functioning on the other laboratory tests. With the exception of and trip by line-induced sedation, side effects were of minor degree. Findings raised questions concerning measuring and improving attentiveness. Differences between results of this and other studies were discussed, as were issues regarding pharmacotherapy with amitriptyline in children.
Communicating risk of medication side effects: An empirical evaluation of EU recommended terminology

Two experiments compared people's interpretation of verbal and numerical descriptions of the risk of medication side effects occurring. The verbal descriptors were selected from those recommended for use by the European Union (very common, common, uncommon, rare, very rare). Both experiments used a controlled empirical methodology, in which nearly 500 members of the general population were presented with a fictitious (but realistic) scenario about visiting the doctor and being prescribed medication, together with information about the medicine's side effects and their probability of occurrence. Experiment 1 found that, in all three age groups tested (18 - 40, 41 - 60 and over 60), participants given a verbal descriptor (very common) estimated side effect risk to be considerably higher than those given a comparable numerical description. Furthermore, the differences in interpretation were reflected in their judgements of side effect severity, risk to health, and intention to comply. Experiment 2 confirmed these findings using two different verbal descriptors (common and rare) and in scenarios which described either relatively severe or relatively mild side effects. Strikingly, only 7 out of 180 participants in this study gave a probability estimate which fell within the EU assigned numerical range. Thus, large scale use of the descriptors could have serious negative consequences for individual and public health. We therefore recommend that the EU and National authorities suspend their recommendations regarding these descriptors until a more substantial evidence base is available to support their appropriate use.
Why are bird migration dates shifting? A review of weather and climate effects on avian migratory phenology

Many studies have reported statistically significant associations between bird migratory phenology and climatic variables, and, consequently, it is mostly accepted that recent shifts in migration dates are a reaction to present climate change. Impacts of weather and climate on departure date, progression and stopover frequency and duration have been reviewed in order to explain the current knowledge of climatic mechanisms underlying such phenological shifts. Climate in departure areas can affect population phenology via the size of the returning population. In a short-term sense, ecological conditions can affect acquisition of migratory body condition during the days preceding departure. Migratory phenology can also be affected by quality and quantity of replaced feathers during moult. Adverse weather conditions en route strongly hinder the progression of individuals and even force them to land. The time spent on stopovers will greatly depend on the ecological conditions there and the opportunities for refuelling. Temperature is by far the climatic variable most frequently related to avian phenology. The use of climatic indices is spreading because they have the advantage of synthesizing weather conditions into a single variable. Remote sensing is probably the best option to explore ecological conditions in areas used by migratory species. Most of the climatic variables employed are from the arrival area, while climate from passage or departure areas is rarely assessed. The overwhelming majority of studies have used variables defined by months, while the use of periods designed ad hoc according to species’ biology is almost anecdotal. It can be concluded that further research is needed to disentangle the true relevance of each type of climatic variable over avian migratory phenology during each phase of migration.
Interpretation of ANOVA models for microarray data using PCA

MOTIVATION ANOVA is a technique, which is frequently used in the analysis of microarray data, e.g. to assess the significance of treatment effects, and to select interesting genes based on P-values. However, it does not give information about what exactly is causing the effect. Our purpose is to improve the interpretation of the results from ANOVA on large microarray datasets, by applying PCA on the individual variance components. Interaction effects can be visualized by biplots, showing genes and variables in one plot, providing insight in the effect of e.g. treatment or time on gene expression. Because ANOVA has removed uninteresting sources of variance, the results are much more interpretable than without ANOVA. Moreover, the combination of ANOVA and PCA provides a simple way to select genes, based on the interactions of interest. RESULTS It is shown that the components from an ANOVA model can be summarized and visualized with PCA, which improves the interpretability of the models. The method is applied to a real time-course gene expression dataset of mesenchymal stem cells. The dataset was designed to investigate the effect of different treatments on osteogenesis. The biplots generated with the algorithm give specific information about the effects of specific treatments on genes over time. These results are in agreement with the literature. The biological validation with GO annotation from the genes present in the selections shows that biologically relevant groups of genes are selected. AVAILABILITY R code with the implementation of the method for this dataset is available from http://www.cac. science.ru. nl under the heading "Software".
How do representations get processed in real nerve cells?

This paper puts forward a general framework for thought about human information processing. It is intended to avoid some of the problems of pipeline or stage models of function. At the same time it avoids the snare of supposing a welter of indefinitely many separate processes. The approach is not particularly original, but rather represents the common elements or presuppositions in a number of modern theories. These presuppositions are not usually explicit, however, and making them so reduces the danger of slipping back into earlier modes of thought. The key point is to distinguish between persisting representations and the processes that translate one representation into another. Various classes or groups of persisting representations can be distinguished by the experimental treatments that interfere with them. In particular, there now seem to be several kinds of short-term or temporary storage, different from each other as well as from longterm memory; the translating processes also have several different modes or kinds. A particularly important aspect of the current position is that a model of this general type no longer requires some external agent to direct and control long sequences of behaviour.
Improved language performance subsequent to low‐frequency rTMS in patients with chronic non‐fluent aphasia post‐stroke

Background: Low‐frequency repetitive transcranial magnetic stimulation (rTMS) has emerged as a potential tool for neurorehabilitation and remediation of language in chronic non‐fluent aphasia post‐stroke. Inhibitory (1 Hz) rTMS has been applied to homologous language sites to facilitate behavioural language changes. Improvements in picture‐naming performance and speech output over time have been reported.
A paradise built in hell: the extraordinary communities that arise in disaster

Rebecca Solnit, 2009 New York, Viking $27.95 (hbk), 368 pp. ISBN 978‐0‐6700‐2107‐9 On a Tuesday afternoon in January 2010, Port‐au‐Prince, Haiti, suffered from one of the most catastrophic earthqua.
The distinction between desires and intentions

Within attitude theory the concepts of desires and intentions are not differentiated but are often treated as synonyms. However, we argue that there are theoretical reasons for distinguishing between desires and intentions, and we articulate three main criteria, perceived performability, action-connectedness, and temporal framing, that differentiate between the two constructs. Two studies are reported to test the distinction. Study 1 (n = 188) revealed that desires, compared to intentions, are less performable, are less connected to actions, and are enacted over longer time frames. Study 2 (n = 249) showed, among other things, that the perceived feasibility for actions that are desired and intended is higher than for those that are only desired, but only when the action refers to relatively short time frames (i.e. 1 week or 4 weeks vs. 4 months). The findings are discussed in the light of the distinction between intentions and desires and the role that they play in individual decision making. Copyright © 2004 John Wiley & Sons, Ltd.
A Combined Retrograde Tracer and GABA‐immunocytochemical Study of the Projection from Nucleus Interpositus Posterior to the Posterior Lobe c2 Zone of the Cat Cerebellum

The extent to which the cells of origin of the cerebellar nucleocortical pathway are immunopositive for γ‐aminobutyric acid (GABA) was investigated in four cats using retrograde labelling of nucleocortical neurons in combination with immunocytochemistry. Neurons were retrogradely labelled by injection of fluorescent (coumarin)‐tagged latex microspheres into the c2 zone in the rostral part of the paramedian lobule. The zone was identified electrophysiologically by the characteristics of the climbing fibre responses evoked on the cerebellar surface by percutaneous stimulation applied to the left and right forepaws in pentobarbitone‐anaesthetized animals. Sections of the cerebellum containing the retrogradely labelled neurons were processed for GABA immunocytochemistty using a fluorescent (rhodamine)‐tagged immunoglobulin. When viewed with epifluorescence microscopy and appropriate filter blocks the retrogradely labelled nucleocortical neurons could be visualized in the same sections as the GABA‐immunopositive neurons. Almost all of a total of 254 labelled nucleocortical neurons were located in nucleus interpositus posterior, where a total of 711 GABAergic neurons were also found. None of these cells contained coumarin‐tagged beads and displayed immunoreactivity for GABA (i.e. none was double‐labelled). When compared by area of their cell body, the nucleocortical and GABA‐immunopositive neurons appeared to form two partially overlapping populations. The mean cell area of the nucleocortical neurons was 620 ± 233 pm2 (SD), whereas the GABA‐immunopositive neurons were much smaller, with a mean cell area of 220 ± 115 pm2. The results suggest that GABA does not play a major role in the nucleocortical pathway to the c2 zone of the rostral paramedian lobule of the cat cerebellum.
The Influence of Occupant Anthropometry and Seat Position on Ejection Risk in a Rollover

Purpose: During rollover crashes, ejection increases an occupant's risk of severe to fatal injury as compared to risks for those retained in the vehicle. The current study examined whether occupant anthropometry might influence ejection risk. Factors such as restraint use/disuse, seating position, vehicle type, and roll direction were also considered in the analysis. Methods: The current study examined occupant ejections in 10 years of National Automotive Sampling System (NASS) single-event rollovers of passenger vehicles and light trucks. Statistical analysis of unweighted and weighted ejection data was carried out. Results: No statistically significant differences in ejection rates were found based on occupant height, age, or body mass index. Drivers were ejected significantly more frequently than other occupants: 62 percent of unrestrained drivers were ejected vs. 51 percent unrestrained right front occupants. Second row unrestrained occupants were ejected at rates similar to right front–seated occupants. There were no significant differences in ejection rates for near- vs. far-side occupants. Conclusions: These data suggest that assessment of ejection prevention systems using either a 50th or 5th percentile adult anthropomorphic test dummy (ATD) might provide a reasonable measure of system function for a broad range of occupants. They also support the development of ejection mitigation technologies that extend beyond the first row to protect occupants in rear seat positions. Future studies should consider potential interaction effects (i.e., occupant size and vehicle dimensions) and the influence of occupant size on ejection risk in non-single-event rollovers.
Clinical and pregnancy outcome following ectopic pregnancy; a prospective study comparing expectancy, surgery and systemic methotrexate treatment

Background. The improved possibility of an early diagnosis of ectopic pregnancy by use of serial quantitative beta‐subunit human chorionic gonadotropin hormone levels together with transvaginal ultrasound has opened up options for conservative treatment. Systemic methotrexate treatment of unruptured ectopic pregnancy has emerged as a safe and effective alternative to surgical procedures. The aim of the present study was to investigate the effectiveness of methotrexate treatment in routine clinical practice, but also to assess pregnancy outcome during a 2.5‐year follow‐up period.
Being a ‘professional’ primary school teacher at the beginning of the 21st century: a comparative analysis of primary teacher professionalism in New Zealand and England

This article analyses findings from two studies conducted collaboratively across two educational settings, New Zealand and England, in 2001–2002. These studies examined the impact of national educational policy reforms on the nature of primary teachers’ work and sense of their own professionalism and compared these impacts across the two countries. Adopting a policy ethnography approach, using in‐depth interview data from samples of teachers in each country, it is argued that there have been discursive shifts in the meaning of the three key terms, autonomy, altruism and knowledge, embodied in the classical professionalism triangle. These shifts reflect policy‐makers’ moves from a ‘professional‐contextualist’ conception of teacher professionalism towards the ‘technocratic‐reductionist’ conception that accompanies neo‐liberal educational reforms in many countries. Teachers in both countries experienced increasing constraints on their autonomy as they became far more subject to ‘extrinsic’ accountability demands. Whether these demands were perceived as enhancing or diminishing teacher professionalism depended on the manner in which they were filtered through the profession’s defining quality, namely teachers’ altruistic concerns for the welfare of the children in their care.
Long- and short-term CDK5 knockdown prevents spatial memory dysfunction and tau pathology of triple transgenic Alzheimer’s mice

CDK5 is a member of the cyclin-dependent kinase family with diverse functions in both the developing and mature nervous system. The inappropriate activation of CDK5 due to the proteolytic release of the activator fragment p25 from the membrane contributes to the formation of neurofibrillary tangles and chronic neurodegeneration. At 18 months of age 3xTg-AD mice were sacrificed after 1 year (long term) or 3 weeks (short term) of CDK5 knockdown. In long-term animals CDK5 knockdown prevented insoluble Tau formation in the hippocampi and prevented spatial memory impairment. In short-term animals, CDK5 knockdown showed reduction of CDK5, reversed Tau aggregation, and improved spatial memory compared to scrambled treated old 3xTg-AD mice. Neither long-term nor short-term CDK5 knock-down had an effect on old littermates. These findings further validate CDK5 as a target for Alzheimer’s disease both as a preventive measure and after the onset of symptoms.
The Meaning of Leprosy and Everyday Experiences: An Exploration in Cirebon, Indonesia

It is imperative to consider the meaning of leprosy and everyday experiences of people affected by leprosy and key persons in the community if one aims to make leprosy services more effective, which appears necessary in Indonesia given the large numbers of new cases detected annually. However, little is written in the international literature about the experiences of people currently being treated for leprosy, those cured, or other key informants. This paper analyses the narratives of the people by drawing upon in-depth interviews with 53 participants and 20 focus groups discussions. The participants were purposively selected. We provide insights into the experiences of people and the meaning they give to leprosy and highlight aspect of aetiology, spirituality, religion, darkening of the skin, and sorcery. We also examine experiences of seeking care and focused on the impact of the disease in particular on the elderly and children. In conclusion, the continued need for implementation of leprosy services in Indonesia is very evident. The diversities in people's experiences with leprosy indicate a demand for responsive leprosy services to serve the diverse needs, including services for those formally declared to be “cured. ”
Human Papilloma Virus: Prevalence, distribution and predictive value to lymphatic metastasis in penile carcinoma.

OBJECTIVES To evaluate the prevalence, distribution and association of HPV with histological pattern of worse prognosis of penile cancer, in order to evaluate its predictive value of inguinal metastasis, as well as evaluation of other previous reported prognostic factors. MATERIAL AND METHODS Tumor samples of 82 patients with penile carcinoma were tested in order to establish the prevalence and distribution of genotypic HPV using PCR. HPV status was correlated to histopathological factors and the presence of inguinal mestastasis. The influence of several histological characteristics was also correlated to inguinal disease-free survival. RESULTS Follow-up varied from 1 to 71 months (median 22 months). HPV DNA was identified in 60.9% of sample, with higher prevalence of types 11 and 6 (64% and 32%, respectively). There was no significant correlation of the histological characteristics of worse prognosis of penile cancer with HPV status. Inguinal disease-free survival in 5 years did also not show HPV status influence (p = 0.45). The only independent pathologic factors of inguinal metastasis were: stage T ≥ T1b-T4 (p = 0.02), lymphovascular invasion (p = 0.04) and infiltrative invasion (p = 0.03). CONCLUSIONS HPV status and distribution had shown no correlation with worse prognosis of histological aspects, or predictive value for lymphatic metastasis in penile carcinoma.
When Is the Hippocampus Involved in Recognition Memory?

The role of the hippocampus in recognition memory is controversial. Recognition memory judgments may be made using different types of information, including object familiarity, an object's spatial location, or when an object was encountered. Experiment 1 examined the role of the hippocampus in recognition memory tasks that required the animals to use these different types of mnemonic information. Rats with bilateral cytotoxic lesions in the hippocampus or perirhinal or prefrontal cortex were tested on a battery of spontaneous object recognition tasks requiring the animals to make recognition memory judgments using familiarity (novel object preference); object–place information (object-in-place memory), or recency information (temporal order memory). Experiment 2 examined whether, when using different types of recognition memory information, the hippocampus interacts with either the perirhinal or prefrontal cortex. Thus, groups of rats were prepared with a unilateral cytotoxic lesion in the hippocampus combined with a lesion in either the contralateral perirhinal or prefrontal cortex. Rats were then tested in a series of object recognition memory tasks. Experiment 1 revealed that the hippocampus was crucial for object location, object-in-place, and recency recognition memory, but not for the novel object preference task. Experiment 2 revealed that object-in-place and recency recognition memory performance depended on a functional interaction between the hippocampus and either the perirhinal or medial prefrontal cortices. Thus, the hippocampus plays a role in recognition memory when such memory involves remembering that a particular stimulus occurred in a particular place or when the memory contains a temporal or object recency component.