Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Hot Water Pretreatment Severity on the Degradation and Enzymatic Hydrolysis of Corn Stover

The effects of hot water pretreatment on the degradation and enzymatic hydrolysis of corn stover were studied. Nearly 100% cellulose recovery in the solid fraction was obtained when corn stover was pretreated at 170°C to 210°C for 3 to 10 min. The highest pretreatment severity of 4.239 (210°C, 10 min) resulted in the highest solid solubilization (37.0%) and xylan solubilization (90.5%). At this severity, inhibitors such as acetic acid, furfural, and hydroxymethyl furfural (HMF) also reached the highest levels of 7.1, 4.6, and 0.6 g L-1, respectively. When the pretreatment temperature was less than 190°C, the furfural concentration was below 1.0 g L-1 and no significant levels of HMF were detected. Enzymatic hydrolysis results showed that increased glucose yields were obtained with increased pretreatment temperatures of corn stover. The highest glucose yield of 89.2% was obtained at the pretreatment severity of 3.716 (210°C, 3 min). Due to the degradation of sugars, a glucose yield of 85.9% was obtained at the highest pretreatment severity of 4.239 (210°C, 10 min).
A call to eradicate non-inclusive terms from the life sciences

Since the Black Lives Matter movement rose to mainstream prominence, the academic enterprise has started recognizing the systematic racism present in science. However, there have been relatively few efforts to make sure that the language used to communicate science is inclusive. Here, I quantify the number of research articles published between 2000 and 2020 that contained non-inclusive terms with racial connotations, such as “blacklist” and “whitelist”, or “master” and “slave”. This reveals that non-inclusive language is being increasingly used in the life sciences literature, and I urge the global academic community to expunge these archaic terms to make science inclusive for everyone.
Immunohistochemical Analysis of DNA Repair- and Drug-Efflux-Associated Molecules in Tumor and Peritumor Areas of Glioblastoma

Glioblastoma (GBM), the most commonly occurring primary tumor arising within the central nervous system, is characterized by high invasiveness and poor prognosis. In spite of the improvement in surgical techniques, along with the administration of chemo- and radiation therapy and the incessant investigation in search of prospective therapeutic targets, the local recurrence that frequently occurs within the peritumoral brain tissue makes GBM the most malignant and terminal type of astrocytoma. In the current study, we investigated both GBM and peritumoral tissues obtained from 55 hospitalized patients and the expression of three molecules involved in the onset of resistance/unresponsiveness to chemotherapy: O6-methylguanine methyltransferase (MGMT), breast cancer resistance protein (BCRP1), and A2B5. We propose that the expression of these molecules in the peritumoral tissue might be crucial to promoting the development of early tumorigenic events in the tissue surrounding GBM as well as responsible for the recurrence originating in this apparently normal area and, accordingly, for the resistance to treatment with the standard chemotherapeutic regimen. Notably, the inverse correlation found between MGMT expression in peritumoral tissue and patients’ survival suggests a prognostic role for this protein.
Blood-brain barrier alterations in human brain tumors revealed by genome-wide transcriptomic profiling.

BACKGROUND Brain tumors, whether primary or secondary, have limited therapeutic options despite advances in understanding driver gene mutations and heterogeneity within tumor cells. The cellular and molecular composition of brain tumor stroma, an important modifier of tumor growth, has been less investigated to date. Only few studies have focused on the vasculature of human brain tumors despite the fact that the blood-brain barrier (BBB) represents the major obstacle for efficient drug delivery. METHODS In this study, we employed RNA sequencing to characterize transcriptional alterations of endothelial cells isolated from primary and secondary human brain tumors. We used an immunoprecipitation approach to enrich for endothelial cells from normal brain, glioblastoma (GBM) and lung cancer brain metastasis (BM). RESULTS Analysis of the endothelial transcriptome showed deregulation of genes implicated in cell proliferation, angiogenesis and deposition of extracellular matrix (ECM) in the vasculature of GBM and BM. Deregulation of genes defining the BBB dysfunction module were found in both tumor types. We identified deregulated expression of genes in vessel-associated fibroblasts in GBM. CONCLUSION We characterize alterations in BBB genes in GBM and BM vasculature and identify proteins that might be exploited for developing drug delivery platforms. In addition, our analysis on vessel-associated fibroblasts in GBM shows that the cellular composition of brain tumor stroma merits further investigation.
Searching and Tracking an Unknown Number of Targets: A Learning-Based Method Enhanced with Maps Merging

Unmanned aerial vehicles (UAVs) have been widely used in search and rescue (SAR) missions due to their high flexibility. A key problem in SAR missions is to search and track moving targets in an area of interest. In this paper, we focus on the problem of Cooperative Multi-UAV Observation of Multiple Moving Targets (CMUOMMT). In contrast to the existing literature, we not only optimize the average observation rate of the discovered targets, but we also emphasize the fairness of the observation of the discovered targets and the continuous exploration of the undiscovered targets, under the assumption that the total number of targets is unknown. To achieve this objective, a deep reinforcement learning (DRL)-based method is proposed under the Partially Observable Markov Decision Process (POMDP) framework, where each UAV maintains four observation history maps, and maps from different UAVs within a communication range can be merged to enhance UAVs’ awareness of the environment. A deep convolutional neural network (CNN) is used to process the merged maps and generate the control commands to UAVs. The simulation results show that our policy can enable UAVs to balance between giving the discovered targets a fair observation and exploring the search region compared with other methods.
Thermal Expansion Behaviors of Bismuth Nanowires

The linear and volumetric thermal expansion coefficients of bismuth nanowire and nanoflower have been measured from 298 to 478 K by high-temperature X-ray diffraction methods. The bismuth nanowire and nanoflower were prepared by a simple solvothermal technique. It was found that the linear and volumetric thermal expansion coefficient of the nanowire decreases initially, then increases, and decreases finally with increasing temperature. The nanowire and nanoflower possess smaller linear thermal expansion coefficient in the a-axis direction in the whole measured temperature range and in the c-axis direction at high temperature as compared to the conventional bulk bismuth. The volumetric expansion coefficients of the nanowire and nanoflower are always smaller than those of the corresponding bulk materials. The results were discussed on the basis of the contributions from point defects, stress, and valence electrons. Our results demonstrated that the anisotropic thermal expansion behavior of bismuth nanowires.
High gene flow in polar cod (Boreogadus saida) from West-Svalbard and the Eurasian Basin.

The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life history approach, and habitat and biophysical dispersal modelling. This article is protected by copyright. All rights reserved.
Clinical study of first-line endocrine therapy for type ER+/PR+ and ER+/PR- advanced breast cancer.

BACKGROUND This study was designed to evaluate the relationship between estrogen receptor (ER) and progesterone receptor (PR) expression status and clinical outcomes in advanced breast cancer patients undergoing first-line endocrine therapy. METHODS Data from 225 advanced breast cancer patients admitted to Henan Cancer Hospital from February 2010 to October 2019 were collected and compared using Chi-squared tests, with Cox regression models being used to identify relevant prognostic factors in these patients. RESULTS PR+ and PR- patients had significantly different median progression-free survival (PFS) times of 25 months (95% CI: 13.50-36.50) and 7 months (95% CI: 4.03-9.97), respectively (P<0.001). Clinical benefit rates (CBR) were also significantly different between these 2 groups (80.9% and 55.6%, respectively; P<0.001). A subgroup analysis of PR+ and PR- patients that underwent aromatase inhibitor (AI) treatment revealed a median PFS of 25.0 months (95% CI: 14.28-35.72) and 7 months (95% CI: 4.18-9.82), respectively (P<0.001), and CBR values of 81.3% and 54.5%, respectively (P<0.001). In addition, for both the whole cohort and the AI subgroup, the total survival of patients with ER+/PR+ breast cancer was longer than that of patients with ER+/PR- breast cancer, and the difference was statistically significant (P<0.001). CONCLUSIONS ER+/PR+ advanced breast cancer patients had a better prognosis than ER+/PR- advanced breast cancer patients undergoing first-line endocrine therapy. In addition, we found that PR status was an independent predictor of first-line endocrine therapy responses in hormone receptor-positive HER2 negative patients.
Secretagogin marks amygdaloid PKCδ interneurons and modulates NMDA receptor availability

Significance Unconscious reactions to threat orchestrated by subcortical brain structures are critical to save the individual at peril. The innate behavioral responses can be modulated by associative learning processes in which the amygdaloid complex gates active motor commands to avoid danger. At the cellular level, glutamatergic neurotransmission through postsynaptic NMDA receptors drives threat-induced changes in synaptic function. Here, we show that the availability of NMDA receptors in the postsynapse is modulated by secretagogin, a Ca2+ sensor protein. Chemogenetic inactivation of secretagogin-expressing neurons, or ablation of secretagogin itself, provides causality for the role of Ca2+-dependent feedback regulation at the cellular level. The perception of and response to danger is critical for an individual’s survival and is encoded by subcortical neurocircuits. The amygdaloid complex is the primary neuronal site that initiates bodily reactions upon external threat with local-circuit interneurons scaling output to effector pathways. Here, we categorize central amygdala neurons that express secretagogin (Scgn), a Ca2+-sensor protein, as a subset of protein kinase Cδ (PKCδ)+ interneurons, likely “off cells. ” Chemogenetic inactivation of Scgn+/PKCδ+ cells augmented conditioned response to perceived danger in vivo. While Ca2+-sensor proteins are typically implicated in shaping neurotransmitter release presynaptically, Scgn instead localized to postsynaptic compartments. Characterizing its role in the postsynapse, we found that Scgn regulates the cell-surface availability of NMDA receptor 2B subunits (GluN2B) with its genetic deletion leading to reduced cell membrane delivery of GluN2B, at least in vitro. Conclusively, we describe a select cell population, which gates danger avoidance behavior with secretagogin being both a selective marker and regulatory protein in their excitatory postsynaptic machinery.
Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as TERT, MLL4, and CCNE1) as well as non-recurrent cancer-related genes (such as CSMD2, NKD2, and RHOU). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.
Analysis of the TORC1 interactome reveals a spatially distinct function of TORC1 in mRNP complexes

This research identifies the interactors of TORC1 by genome-wide BiFC screens and reveals that a spatially distinct portion of TORC1 interacts with RNA-binding proteins. As a component of mRNP complexes, TORC1 phosphorylates Scd6 to negatively regulate Scd6 activity in translational repression and P-body accumulation.
Social impairment in relation to clinical symptoms in youth at high risk for bipolar disorder

Social impairment is common in individuals with bipolar disorder (BD), although its role in youths at high‐risk for BD (i.e., mood symptoms in the context of a family history of BD) is not well understood. Social impairment takes many forms including social withdrawal, relational aggression, physical aggression, and victimization. The aim of this study was to explore the links between social impairment and clinical symptoms in youth at high‐risk for BD.
Spermine and Spermidine Priming against Botrytis cinerea Modulates ROS Dynamics and Metabolism in Arabidopsis

Polyamines (PAs) are ubiquitous small aliphatic polycations important for growth, development, and environmental stress responses in plants. Here, we demonstrate that exogenous application of spermine (Spm) and spermidine (Spd) induced cell death at high concentrations, but primed resistance against the necrotrophic fungus Botrytis cinerea in Arabidopsis. At low concentrations, Spm was more effective than Spd. Treatments with higher exogenous Spd and Spm concentrations resulted in a biphasic endogenous PA accumulation. Exogenous Spm induced the accumulation of H2O2 after treatment but also after infection with B. cinerea. Both Spm and Spd induced the activities of catalase, ascorbate peroxidase, and guaiacol peroxidase after treatment but also after infection with B. cinerea. The soluble sugars glucose, fructose, and sucrose accumulated after treatment with high concentrations of PAs, whereas only Spm induced sugar accumulation after infection. Total and active nitrate reductase (NR) activities were inhibited by Spm treatment, whereas Spd inhibited active NR at low concentrations but promoted active NR at high concentrations. Finally, γaminobutyric acid accumulated after treatment and infection in plants treated with high concentrations of Spm. Phenylalanine and asparagine also accumulated after infection in plants treated with a high concentration of Spm. Our data illustrate that Spm and Spd are effective in priming resistance against B. cinerea, opening the door for the development of sustainable alternatives for chemical pesticides.
Reduction in rectal doses of pelvic radiotherapy with excessive rectal gas extraction: a single-institution case report.

During radiotherapy for pelvic tumors, there might be insufficient radiation doses delivered that result from concerns of immediately adjacent critical organs, most notebly the rectum. Several measures have been proposed to reduce the rectal doses, such as use of a radioprotective spacer to shift the rectum away from the lesion or an endorectal balloon to reduce the internal target volume (ITV). The removal of rectal gas is supposed to achieve the similar effect by reducing the rectal volume and ITV. This is because the distance of the rectum to lesions can be increased with decreasing rectal volumes, which also makes it easy for physicists to avoid the rectum during field design. Besides, a reduced ITV can be obtained due to stability in rectal volume, as with use of an endorectal balloon. The procedure is most suitable for patients receiving stereotactic body radiotherapy (SBRT) and high dose rate brachytherapy (HDR-BR) because of limited treatment sessions. In this study, we showed that the rectal dose decreased significantly with rectal gas extraction, as manifested by dose parameters of D2 cm3 and D0.1 cm3 (The doses delivered to the most exposed 2 cm, 3 and 0.1 cm3 of the rectum, respectively). This technique is especially benefitable for candidates with excessive rectal gas fillings.
The Curious Case of the “Neurotoxic Skink”: Scientific Literature Points to the Absence of Venom in Scincidae

In contrast to the clearly documented evolution of venom in many animal lineages, the origin of reptilian venom is highly debated. Historically, venom has been theorised to have evolved independently in snakes and lizards. However, some of the recent works have argued for the common origin of venom in “Toxicofera” reptiles, which include the order Serpentes (all snakes), and Anguimorpha and Iguania lizards. Nevertheless, in both these contrasting hypotheses, the lizards of the family Scincidae are considered to be harmless and devoid of toxic venoms. Interestingly, an unusual clinical case claiming neurotoxic envenoming by a scincid lizard was recently reported in Southern India. Considering its potentially significant medicolegal, conservation and evolutionary implications, we have summarised the scientific evidence that questions the validity of this clinical report. We argue that the symptoms documented in the patient are likely to have resulted from krait envenomation, which is far too frequent in these regions.
Fatigue Failure from Inner Surfaces of Additive Manufactured Ti-6Al-4V Components

Selective laser melting (SLM) is an additive manufacturing process for producing metallic components with complex geometries. A drawback of this process is the process-inherent poor surface finish, which is highly detrimental in materials submitted to fatigue loading situations. The goal of this work is to analyze the fatigue behavior of Ti-6Al-4V specimens with internal axial channels under the following different conditions: hole drilled, hole as manufactured, and hole threaded M4 × 0.7. All the cases studied showed a lower fatigue performance as compared with solid samples due to the surface roughness and geometry effect that produced a surface stress concentration leading to a reduction in fatigue strength. The fractography revealed that crack initiation occurred from the internal surface in all specimens with internal channel mostly from defects as unfused particles and lack of fusion zones, while for the solid specimens crack initiation was observed from the external surface due to insufficient fusion defect. The application of the Smith-Watson-Topper energy-based parameter was revealed to be a good tool for fatigue life prediction of the different series studied.
Attention-Dependent Physiological Correlates in Sleep-Deprived Young Healthy Humans

Cognitive functions could be specifically altered but masked from the unspecific effect of workload, a common factor affecting cognitive functions that modulate peripheral outputs. To identify workload-related and specific, task-dependent components, physiological correlates of cognitive functioning were derived by studying 15 healthy volunteers performing attentional tasks in baseline and post-sleep-deprivation conditions (one week interval). Sleep deprivation was introduced to increase workload. We performed recordings of heart pulse, facial temperature, and head movements during tasks assessing attentional network efficiency (ANT, Attentional Network Task; CCT, Continuous Compensatory Tracker) workload assessments after execution of tasks. Changes in cognitive and physiological indices were studied in both conditions; physiological correlates of cognitive performance were identified by correlating changes from baseline to post-sleep-deprivation condition of task indices with those of physiological measures after correction for between-conditions workload changes. We found that mental and physical demands of workload increased after sleep deprivation. We identified no changes in cognitive and physiological indices across conditions; specific physiological correlates of attentional systems, as indicated by the negative correlation between changes in ANT-alerting and changes in amplitude of head movements and the positive correlation between changes in CCT-speed indexing alertness and changes in facial temperature.
Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4‐related disease

Nager syndrome epitomizes the acrofacial dysostoses, which are characterized by craniofacial and limb defects. The craniofacial defects include midfacial retrusion, downslanting palpebral fissures, prominent nasal bridge, and micrognathia. Limb malformations typically include hypoplasia or aplasia of radial elements including the thumb. Nager syndrome is caused by haploinsufficiency of SF3B4, encoding a spliceosomal protein called SAP49. Here, we report a patient with a loss of function variant in SF3B4 without acrofacial dysostosis or limb defects, whose reason for referral was developmental and growth delay. This patient is evidence of a broader phenotypic spectrum associated with SF3B4 variants than previously appreciated.