Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of peer separation in young chimpanzees (Pan troglodytes)

Ten chimpanzees (Pan troglogytes), aged 18–24 months, housed without mothers as two dyads and two triads, were subjected to social separation. Two issues were addressed: the effects of peer separation in chimpanzees; and differential responses by subjects living in dyads compared with those living in triads. Chimpanzees that were alone during separation reacted with high levels of “protest” alternating with “despair” throughout the separation period. The continued presence of one cagemate, during separation from a third, was a strong mitigating factor. Even when the primary attachment was formed with the absent cagemate, the remaining chimpanzees clung to each other and the levels of protest and despair, when present, were low. Upon reunion, neither “detachment” nor heightened levels of clinging were conspicuous, but there was increased social interaction. The data on separation of chimpanzees are intermediate between those of humans and monkeys separated from mothers or peers. The increased social interactions during reunion, including looking, are comparable to the visual vigilance reported for humans.
A candidate culture-dependent form in apes, nut-cracking, can be individually learnt by naïve orangutans (Pongo abelii)

Several species of non-human apes have been suggested to rely on copying to acquire some of their behavioural forms. One of the most cited examples - and UN-protected - is nut-cracking in chimpanzees. However, copying might not be the most parsimonious explanation for nut-cracking, considering the lack of evidence for spontaneous copying in this species. The zone of latent solutions (ZLS) hypothesis argues instead that the behavioural form of nut-cracking is individually learnt, whilst non-copying social learning fosters frequency differences across populations. In order to differentiate between the copying and the ZLS hypothesis, four nut-cracking-naive orangutans (Mage=16; age range=10-19; 4F; at time of testing) were provided with nuts and hammers but were not demonstrated the behaviour. Whilst the adults in the group were able to open nuts with their teeth, one juvenile spontaneously expressed nut-cracking with a wooden hammer. We therefore show that the behavioural form of nut-cracking does not necessarily rely on copying in orangutans.
A phylogenetic analysis of the adipokinetic neuropeptides of Ensifera

Abstract. Adipokinetic neuropeptides, from the corpora cardiaca of various species of the suborder Ensifera, encompassing members of all superfamilies (except the Gryllacridoidea), were isolated by liquid chromatography, and identified structurally by comparison of retention times and mass spectrometry data with respect to information from known members of this peptide family. Ensiferan species always contain only one adipokinetic hormone (AKH) peptide, as assessed for a few species by monitoring typical AKH mass peaks from a crude corpora cardiaca extract. This AKH is an octapeptide, and is either Scg‐AKH‐II (pGlu‐Leu‐Asn‐Phe‐Ser‐Thr‐Gly‐Trp amide) which occurs in all Tettigoniidea (except Schizodactyloidea) and in Gryllotalpoidea, or Grb‐AKH (pGlu‐Val‐Asn‐Phe‐Ser‐Thr‐Gly‐Trp amide) which occurs in Grylloidea (except Gryllotalpoidea) and Schizodactyloidea. Using the structural information of these neuropeptides in conjunction with morpho‐anatomical characters, these data are interpreted in a phylogenetic framework. The lack of a decapeptide and the presence of the octapeptide Scg‐AKH‐II are ancestral in Ensifera. The ancestral Scg‐AKH‐II twice underwent an independent and convergent modification to Grb‐AKH.
Cerebral cavernous malformation 1 determines YAP/TAZ signaling dependent metastatic hallmarks of prostate cancer cells

Enhanced Yes-associated protein (YAP)/transcriptional co-activator with PDZ-binding motif (TAZ) signaling is correlated with the extraprostatic extension of prostate cancer. However, the mechanism by which YAP/TAZ signaling becomes hyperactive and drives prostate cancer progression is currently unclear. In this study, we demonstrated that CCM1 induces the metastasis of multiple types of prostate cancer cells by regulating YAP/TAZ signaling. Mechanistically, CCM1, a gene mutated in cerebral cavernous malformation, suppresses DDX5, which regulates the PLK1-mediated suppression of YAP/TAZ signaling, indicating that CCM1 and DDX5 are novel upstream regulators of YAP/TAZ signaling. We also revealed that higher expression of CCM1, which is uniquely found in advanced prostate cancer, is inversely correlated with metastasis-free and overall survival in patients with prostate cancer. Our findings highlight the importance of CCM1-DDX5-PLK1-YAP/TAZ signaling in the metastasis of prostate cancer cells. Statement of Significance Our analysis of CCM1 expression and function represents a candidate predictive biomarker for prostate cancer metastasis and provides an evidence that abnormality of CCM1 can be pathogenic in prostate cancer. Importantly, CCM1 regulation of metastasis progression appears to a common molecular event in metastatic prostate cancer cells arising in disparate genetic backgrounds.
Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage

Significance Glioblastoma is a highly lethal form of brain cancer with no current treatment options that substantially improve patient outcomes. A key therapeutic challenge is the identification of methods that reduce tumor burden while leaving normal cells unaffected. We show that TERT-promoter mutations, common in glioblastoma, lead to TERT reactivation through increased binding of GABPB1L-isoform–containing transcription factor complexes. In turn, we find that cancer-cell–specific inhibition of TERT through GABPB1L reduction results in near-term anti-growth effects and an impaired DNA damage response that profoundly increase the sensitivity of glioblastoma tumors to frontline chemotherapy. Our results thus provide rationale for GABPB1L inhibition combined with temozolomide chemotherapy treatment as a promising therapeutic strategy for glioblastoma. Most glioblastomas (GBMs) achieve cellular immortality by acquiring a mutation in the telomerase reverse transcriptase (TERT) promoter. TERT promoter mutations create a binding site for a GA binding protein (GABP) transcription factor complex, whose assembly at the promoter is associated with TERT reactivation and telomere maintenance. Here, we demonstrate increased binding of a specific GABPB1L-isoform–containing complex to the mutant TERT promoter. Furthermore, we find that TERT promoter mutant GBM cells, unlike wild-type cells, exhibit a critical near-term dependence on GABPB1L for proliferation, notably also posttumor establishment in vivo. Up-regulation of the protein paralogue GABPB2, which is normally expressed at very low levels, can rescue this dependence. More importantly, when combined with frontline temozolomide (TMZ) chemotherapy, inducible GABPB1L knockdown and the associated TERT reduction led to an impaired DNA damage response that resulted in profoundly reduced growth of intracranial GBM tumors. Together, these findings provide insights into the mechanism of cancer-specific TERT regulation, uncover rapid effects of GABPB1L-mediated TERT suppression in GBM maintenance, and establish GABPB1L inhibition in combination with chemotherapy as a therapeutic strategy for TERT promoter mutant GBM.
Human CD8+ T Cells Exhibit a Shared Antigen Threshold for Different Effector Responses

Key Points CD8+ T cells produce TNF-α, IL-2, and IFN-γ with similar Ag thresholds. Costimulation decreases Ag thresholds similarly for different cytokines. A common rate-limiting switch downstream of the TCR can explain these findings. Visual Abstract T cells recognizing cognate pMHC Ags become activated to elicit a myriad of cellular responses, such as target cell killing and the secretion of different cytokines, that collectively contribute to adaptive immunity. These effector responses have been hypothesized to exhibit different Ag dose and affinity thresholds, suggesting that pathogen-specific information may be encoded within the nature of the Ag. In this study, using systematic experiments in a reductionist system, in which primary human CD8+ T cell blasts are stimulated by recombinant peptides presented on MHC Ag alone, we show that different inflammatory cytokines have comparable Ag dose thresholds across a 25,000-fold variation in affinity. Although costimulation by CD28, CD2, and CD27 increased cytokine production in this system, the Ag threshold remained comparable across different cytokines. When using primary human memory CD8+ T cells responding to autologous APCs, equivalent thresholds were also observed for different cytokines and killing. These findings imply a simple phenotypic model of TCR signaling in which multiple T cell responses share a common rate-limiting threshold and a conceptually simple model of CD8+ T cell Ag recognition, in which Ag dose and affinity do not provide any additional response-specific information.
The African Acacias - A thorny subject

Abstract There are 129 Acacia species in Africa. They are intermediate in plant succession and colonize degraded land. They restore fertility and can be maintained indefinitely in agricultural systems. They provide many benefits but are disliked for their thorns and invasiveness. Seed was collected across the ranges of Acacia erioloba, A karroo, A nilotica, A.senegal, A. tortilis and Faidherbia (formerly Acacia) albida. Screening trials indicated that, with selection, all had potential both inside and outside their natural ranges. Subsidiary studies showed that some acacias obtain their nitrogen from groundwater rather than from the atmosphere, that they can produce more crude protein per hectare than a grain crop, that there are annual rings in the wood, and that gum arabic could be a lucrative cash crop. Farmers will resist planting acacias until the benefits can be translated into cash. The challenge for breeders in the new millennium is to produce trees that are inherently so good that they sell themselves to the farmer.
An automated homecage system for multiwhisker detection and discrimination learning in mice

Automated, homecage behavioral training for rodents has many advantages: it is low stress, requires little interaction with the experimenter, and can be easily manipulated to adapt to different experimental condition. We have developed an inexpensive, Arduino-based, homecage training apparatus for sensory association training in freely-moving mice using multiwhisker air current stimulation coupled to a water reward. Animals learn this task readily, within 1-2 days of training, and performance progressively improves with training. We examined the parameters that regulate task acquisition using different stimulus intensities, directions, and reward valence. Learning was assessed by comparing anticipatory licking for the stimulus compared to the no-stimulus (blank) trials. At high stimulus intensities (>9 psi), animals showed markedly less participation in the task. Conversely, very weak air current intensities (1-2 psi) were not sufficient to generate rapid learning behavior. At intermediate stimulus intensities (5-6 psi), a majority of mice learned that the multiwhisker stimulus predicted the water reward after 24-48 hrs of training. Both exposure to isoflurane and lack of whiskers decreased animals’ ability to learn the task. Perceptual learning was assessed and following training at an intermediate stimulus intensity, perception was likely heightened as mice were able to transfer learning behavior when exposed to the lower stimulus intensity. Mice learned to discriminate between two directions of stimulation rapidly and accurately, even when the angular distance between the stimuli was <15 degrees. Switching the reward to a more desirable reward, aspartame, had little effect on learning trajectory. Our results show that a tactile association task in an automated homecage environment can be monitored by anticipatory licking to reveal rapid and progressive behavioral change. These Arduino-based, automated mouse cages enable high-throughput training that facilitate analysis of large numbers of genetically modified mice with targeted manipulations of neural activity.
scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets

In gene expression profiling studies, including single-cell RNA-seq (scRNAseq) analyses, the identification and characterization of co-expressed genes provides critical information on cell identity and function. Gene co-expression clustering in scRNA-seq data presents certain challenges. We show that commonly used methods for single cell data are not capable of identifying co-expressed genes accurately, and produce results that substantially limit biological expectations of co-expressed genes. Herein, we present scLM, a gene co-clustering algorithm tailored to single cell data that performs well at detecting gene clusters with significant biologic context. scLM can simultaneously cluster multiple single-cell datasets, i.e. consensus clustering, enabling users to leverage single cell data from multiple sources for novel comparative analysis. scLM takes raw count data as input and preserves biological variations without being influenced by batch effects from multiple datasets. Results from both simulation data and experimental data demonstrate that scLM outperforms the existing methods with considerably improved accuracy. To illustrate the biological insights of scLM, we apply it to our in-house and public experimental scRNA-seq datasets. scLM identifies novel functional gene modules and refines cell states, which facilitates mechanism discovery and understanding of complex biosystems such as cancers. A user-friendly R package with all the key features of the scLM method is available at https://github.com/QSong-WF/scLM.
Representational pattern similarity of electrical brain activity reveals rapid and specific prediction during language comprehension

Predicting upcoming stimuli and events is a critical function of the brain, and understanding the mechanisms of prediction has thus become a central topic in neuroscientific research. Language provides a fertile testing ground for examining predictive mechanisms, as comprehenders use context to predict different features of upcoming words. Although there is a substantive body of research on prediction in language, many aspects of the mechanisms of prediction remain elusive, in part due to a lack of methodological tools to probe prediction formation in the moment. To elucidate what features are neurally pre-activated and when, we used representational similarity analysis (RSA) on data from a sentence reading task (Federmeier et al., 2007). We compared EEG activity patterns elicited by expected and unexpected sentence final words to patterns from the preceding words of the sentence, in both strongly and weakly constraining sentences. Pattern similarity with the final word was increased in an early time window (suggestive of visual feature activation) following the presentation of the pre-final word, and this increase was modulated by both expectancy and constraint (greatest for strongly constrained expected words). This was not seen at earlier words, suggesting that predictions are precisely timed. Additionally, pre-final word activity – the predicted representation - had negative similarity with later final word activity, but only for strongly expected words. Together, these findings shed light on the mechanisms of prediction in the brain: features of upcoming stimuli are rapidly pre-activated following related cues, but the predicted information may receive reduced subsequent processing upon confirmation.
Greenhouse conditions in lower Eocene coastal wetlands?—Lessons from Schöningen, Northern Germany

The Paleogene succession of the Helmstedt Lignite Mining District in Northern Germany includes coastal peat mire records from the latest Paleocene to the middle Eocene at the southern edge of the Proto-North Sea. Therefore, it covers the different long- and short-term climate perturbations of the Paleogene greenhouse. 56 samples from three individual sections of a lower Eocene seam in the record capture the typical succession of the vegetation in a coastal wetland during a period that was not affected by climate perturbation. This allows facies-dependent vegetational changes to be distinguished from those that were climate induced. Cluster analyses and NMDS of well-preserved palynomorph assemblages reveal four successional stages in the vegetation during peat accumulation: (1) a coastal vegetation, (2) an initial mire, (3) a transitional mire, and (4) a terminal mire. Biodiversity measures show that plant diversity decreased significantly in the successive stages. The highly diverse vegetation at the coast and in the adjacent initial mire was replaced by low diversity communities adapted to wet acidic environments and nutrient deficiency. The palynomorph assemblages are dominated by elements such as Alnus (Betulaceae) or Sphagnum (Sphagnaceae). Typical tropical elements which are characteristic for the middle Eocene part of the succession are missing. This indicates that a more warm-temperate climate prevailed in northwestern Germany during the early lower Eocene.
Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes

Significant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the “ecology” of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influence the distribution of eDNA in lakes. We sampled eDNA depth profiles of five dimictic lakes during both summer stratification and autumn turnover, each containing warm- and cool-water fishes as well as the cold-water stenotherm, lake trout (Salvelinus namaycush). Habitat use by lake trout was validated by acoustic telemetry and was significantly related to eDNA distribution during stratification. Fish eDNA became “stratified” into layers during summer months, reflecting lake stratification and the thermal niches of the species. During summer months, lake trout, which rarely ventured into shallow waters, could only be detected at the deepest layers of the lakes, whereas the eDNA of warm-water fishes was much more abundant above the thermocline. By contrast, during autumn lake turnover, the fish species assemblage as detected by eDNA was homogenous throughout the water column. These findings contribute to our overall understanding of the “ecology” of eDNA within lake ecosystems, illustrating how the strong interaction between seasonal thermal structure in lakes and thermal niches of species on very localised spatial scales influences our ability to detect species.
Widespread variation in heat tolerance of the coral Acropora hyacinthus spanning variable thermal regimes across Palau

Climate change is poised to dramatically change ecosystem composition and productivity, leading scientists to consider the best approaches to fostering population resilience and diversity in the face of these changes. Here we present results of a large-scale experimental assessment of bleaching resistance, a critical trait for coral population persistence as oceans warm, in 293 colonies of the coral Acropora hyacinthus across 39 reefs in Palau. We find bleaching resistant individuals originate significantly more often from warmer reefs, although they inhabit almost every reef regardless of temperature at low frequency. High levels of variation within reefs, where colonies experience similar temperatures, suggests that bleaching resistance is not solely due to phenotypic plasticity, but also involves adaptive alleles and host-symbiont interactions. To the extent that it is heritable, bleaching resistance could be used in promoting nursery growth, habitat restoration, or breeding, while employing large numbers of resistant colonies to preserve genetic variation.
Elemental composition of oat groats

Concentrations of P, K, Mg, Fe, Zn, and Mn were determined by emission spectroscopy in groats from slx cultivars of oats (Auena satiua L.) grown in 1971 and 1972. For 1972, data were also obtained for Ca, Cu, B, and Ba. Protein concentration and groat weight were determined both years. Univariate analyses of variance revealed significant differences among cultivars for each element, protein, and groat weight. Multivariate analysis of variance indicated significant differences among cultivar mean vectors. The close association between multivariate analysis of vanance and partitioning of the covariances is pointed out. Positive genotypic correlations were obtained among elemental and protein concentrations, but elemental and protein concentrations were negatively correlated with groat weight. Bran contained higher elementai concentrations than endosperm, and differences among cultivars in per cent bran probably accounted for the positive correlations among elements.
Effect of dietary protein level on growth and food utilization in juvenile Murray cod Maccullochella peelii peelii (Mitchell).

Murray cod Maccullochella peelii peelii (Mitchell) is a freshwater Percichthyid fish considered to have high culture potential. Growth and feed utilization were examined in a 56-day experiment, in which triplicate groups of juvenile Murray cod (initial weight 21.5 ± 0.03 g) were fed isocalorific diets (gross energy content of about 21 kJ g−1) containing 40%, 45%, 50%, 55% or 60% protein (designated P40, P45, etc.). Final mean weight, percentage increase in weight and specific growth rate (SGR; % day−1) were highest in fish fed the P50 diet. Food conversion ratio (FCR; 1.05 ± 0.04) and protein efficiency ratio (PER; 1.98 ± 0.11) were also best in fish on the P50 diet, but the differences in these parameters from the corresponding values on diets P55 and P60 were not always significant. FCR (Y) was related to dietary protein content (X), the relationship being a second-order polynomial, in which Y = 0.004X2−0.431X + 12.305 (r= 0.95; P < 0.01). The proportions of carcass moisture, protein, lipid and ash did not differ among the different dietary treatments. The protein conversion efficiency (y) was negatively correlated to percentage dietary protein (X) content, the relationship being: y = 62.76–0.62X (r= 0.99; P < 0.01).
Long range vertical migration of Volvox in tropical Lake Cahora Bassa (Mozambique)

Volvox sp. performed diel vertical migrations in Lake Cahora Bassa, the amplitude of which greatly exceeded those reported for other species of freshwater algae. Migration velocities even exceeded the maxima attained by marine dinoflagellates. The daytime depth distribution is attributed to the light regime and the nighttime depth distribution to phosphorus uptake in deeper water layers.
Pathogenic ability of bipolaris sorokiniana in relation to spring barley (Hordeum vulgare)

The transmission efficiency of Bipolaris sorokiniana from grain to the first leaf tips and effect of plant infection time on germination and chemical components of harvested seeds was investigated. Infected grain derived from plants of five spring barley cultivars inoculated by spraying with fungal spore suspension at four development stages: tillering, stem elongation, heading and flowering. The fungus was detected in symptomless first leaf tips of seedling beginning from seven days after sowing and reaching the maximum infection incidence on the second week. Infection incidence subsequently decreased progressively to the end of the trial. Most infected grain were harvested from plants inoculated at the latest terms: heading and flowering. Grain infection by B. sorokiniana influenced germination capacity. Grain strongly infected by the pathogen (about 81–86%) germinated worse (75–77%) than less infected (93%). The content of protein, fiber and starch in kernels depended significantly on time of plant inoculation and grain infection by B. sorokiniana.