Miracle-dz/UniFAR-FTUs huggingface dataset:
Receiver-Side TCP Countermeasure in Cellular Networks

Cellular-based networks keep large buffers at base stations to smooth out the bursty data traffic, which has a negative impact on the user’s Quality of Experience (QoE). With the boom of smart vehicles and phones, this has drawn growing attention. For this paper, we first conducted experiments to reveal the large delays, thus long flow completion time (FCT), caused by the large buffer in the cellular networks. Then, a receiver-side transmission control protocol (TCP) countermeasure named Delay-based Flow Control algorithm with Service Differentiation (DFCSD) was proposed to target interactive applications requiring high throughput and low delay in cellular networks by limiting the standing queue size and decreasing the amount of packets that are dropped in the eNodeB in Long Term Evolution (LTE). DFCSD stems from delay-based congestion control algorithms but works at the receiver side to avoid the performance degradation of the delay-based algorithms when competing with loss-based mechanisms. In addition, it is derived based on the TCP fluid model to maximize the network utility. Furthermore, DFCSD also takes service differentiation into consideration based on the size of competing flows to shorten their completion time, thus improving user QoE. Simulation results confirmed that DFCSD is compatible with existing TCP algorithms, significantly reduces the latency of TCP flows, and increases network throughput.
Low-Power Distributed Data Flow Anomaly-Monitoring Technology for Industrial Internet of Things

In recent years, the industrial use of the internet of things (IoT) has been constantly growing and is now widespread. Wireless sensor networks (WSNs) are a fundamental technology that has enabled such prevalent adoption of IoT in industry. WSNs can connect IoT sensors and monitor the working conditions of such sensors and of the overall environment, as well as detect unexpected system events in a timely and accurate manner. Monitoring large amounts of unstructured data generated by IoT devices and collected by the big-data analytics systems is a challenging task. Furthermore, detecting anomalies within the vast amount of data collected in real time by a centralized monitoring system is an even bigger challenge. In the context of the industrial use of the IoT, solutions for monitoring anomalies in distributed data flow need to be explored. In this paper, a low-power distributed data flow anomaly-monitoring model (LP-DDAM) is proposed to mitigate the communication overhead problem. As the data flow monitoring system is only interested in anomalies, which are rare, and the relationship among objects in terms of the size of their attribute values remains stable within any specific period of time, LP-DDAM integrates multiple objects as a complete set for processing, makes full use of the relationship among the objects, selects only one “representative” object for continuous monitoring, establishes certain constraints to ensure correctness, and reduces communication overheads by maintaining the overheads of constraints in exchange for a reduction in the number of monitored objects. Experiments on real data sets show that LP-DDAM can reduce communication overheads by approximately 70% when compared to an equivalent method that continuously monitors all objects under the same conditions.
Malaria: The Past and the Present

Malaria is a severe disease caused by parasites of the genus Plasmodium, which is transmitted to humans by a bite of an infected female mosquito of the species Anopheles. Malaria remains the leading cause of mortality around the world, and early diagnosis and fast-acting treatment prevent unwanted outcomes. It is the most common disease in Africa and some countries of Asia, while in the developed world malaria occurs as imported from endemic areas. The sweet sagewort plant was used as early as the second century BC to treat malaria fever in China. Much later, quinine started being used as an antimalaria drug. A global battle against malaria started in 1955, and Croatia declared 1964 to be the year of eradication of malaria. The World Health Organization carries out a malaria control program on a global scale, focusing on local strengthening of primary health care, early diagnosis of the disease, timely treatment, and disease prevention. Globally, the burden of malaria is lower than ten years ago. However, in the last few years, there has been an increase in the number of malaria cases around the world. It is moving towards targets established by the WHO, but that progress has slowed down.
A site visit protocol for assessing recovery promotion at the program level: An example from the Veterans Health Administration.

OBJECTIVE A site visit protocol was developed to assess recovery promotion in the organizational climate and culture of programs for veterans with serious mental illnesses. METHOD The protocol was pilot-tested in 4 programs: 2 that had scored high on the pilot version of a staff survey measure of program-level recovery promotion and 2 that had scored low. Two-person teams conducted onsite visits and assigned global and organizational domain ratings. Interrater agreement was assessed by examining adjacent agreement and computing weighted kappa. RESULTS The on-site protocol had good interrater agreement and discriminated between sites that scored high and low on the staff survey. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE This site visit protocol and procedure shows promise for evaluating recovery promotion in milieu-based programs. After further refinement of this tool, adaptations could be developed for accreditation protocols or for program self-assessment and quality improvement efforts. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Lexical Richness, a reliable measure of Intermediate L2 Learners’ current status of acquisition of English language

This article aims to explore the utility of the relationship between lexical richness and size as an indicator of acquisition status of English language of L2 learners of intermediate level, having rural background on the basis of their self -written output. 126 students’ essays were used to measure the lexical richness (126 students of Sem-I and 63 students of Sem-II) Lexical Frequency Profile was used to sort it out. Its values discriminated students of different proficiency level and displayed L2 Learners vocabulary size in use. LFP result’s consistency and legitimacy was obtained by comparing its result with an independent and separate measure of vocabulary size, VLT. The result showed that lexical richness has a direct link with vocabulary size (receptive vocabulary) of L2 learners. It discusses the utility of the inference based on the lexical richness of L2’s written text for monitoring purpose of language acquisition process of L2 learners and to determine appropriate strategies for the desired growth of vocabulary size.
A Multiple-Mechanism Developmental Model for Defining Self-Organizing Geometric Structures

This thesis introduces a model of multicellular development. The model combines elements of the chemical, cell lineage, and mechanical models of morphogenesis pioneered by Turing, Lindenmayer, and Odell, respectively. The internal state of each cell in the model is represented by a time-varying state vector that is updated by a differential equation. The differential equation is formulated as a sum of contributions from different sources, describing gene transcription, kinetics, and cell metabolism. Each term in the differential equation is multiplied by a conditional expression that models regulatory processes specific to the process described by that term. The resulting model has a broader range of fundamental mechanisms than other developmental models. Since gene transcription is included, the model can represent the genetic orchestration of a developmental process involving multiple mechanisms. We show that a computational implementation of the model represents a wide range of biologically relevant phenomena in two and three dimensions. This is illustrated by a diverse collection of simulation experiments exhibiting phenomena such as lateral inhibition, differentiation, segment formation, size regulation, and regeneration of damaged structures. We have explored several application areas with the model: Synthetic biology. We advocate the use of mathematical modeling and simulation for generating intuitions about complex biological systems, in addition to the usual application of mathematical biology to perform analysis on a simplified model. The breadth of our model makes it useful as a tool for exploring biological questions about pattern formation and morphogenesis. We show that simulated experiments to address a particular question can be done quickly and can generate useful biological intuitions. As an example, we document a simulation experiment exploring inhibition via surface chemicals. This experiment suggests that the final pattern depends strongly on the temporal sequence of events. This intuition was obtained quickly using the simulator as an aid to understanding the general behavior of the developmental system. Artificial evolution of neural networks. Neural networks can be represented using a developmental model. We investigate the use of artificial evolution to select equations and parameters that cause the model to create desired structures. We compare our approach to other work in evolutionary neural networks, and discuss the difficulties involved. Computer graphics modeling. We extend the model to allow cells to sense the presence of a 3D surface model, and then use the multicellular simulator to grow cells on the surface. This database amplification technique enables the creation of cellular textures to represent detailed geometry on a surface (e.g., scales, feathers, thorns). In the process of writing many developmental programs, we have gained some experience in the construction of self-organizing cellular structures. We id
Localization of Glucagon-like Peptide-2 Receptor Expression in the Mouse.

Glucagon-like peptide-2 (GLP-2), secreted from enteroendocrine cells, attenuates gut motility, enhances barrier function, and augments nutrient absorption, actions mediated by a single GLP-2 receptor (GLP-2R). Despite extensive analyses, the precise distribution and cellular localization of GLP-2R expression remains controversial, confounded by the lack of suitable GLP-2R antisera. Here we reassessed murine Glp2r expression using regular and quantitative Real-Time PCR (qPCR), in situ hybridization (ISH), and a Glp2rLacZ reporter mouse. Glp2r mRNA expression was detected from the stomach to the rectum, and most abundant in the jejunum. Glp2r transcripts were also detected in mesenteric lymph nodes, gallbladder, urinary bladder, and mesenteric fat. Surprisingly, Glp2r mRNA was found in testis by qPCR at levels similar to jejunum. However, the testis Glp2r transcripts detected by different primer pairs and qPCR lacked 5' mRNA coding sequences and only a minute proportion of them corresponded to full-length Glp2r mRNA. Within the gut, Glp2r driven Lacz expression was localized to enteric neurons and lamina propria stromal cells, findings confirmed by ISH analysis of the endogenous Glp2r mRNA. Unexpectedly, vascular Glp2rLacZ expression was localized to mesenteric veins, and not arteries. Moreover, mesenteric fat Glp2rLacZ expression was detected within blood vessels, and not adipocytes. Reporter LacZ expression was not detected in all tissues expressing an endogenous Glp2r transcript, such as gallbladder, urinary bladder and mesenteric lymph nodes. Collectively, these findings extend our understanding of the cellular domains of Glp2r expression, and highlight limitations inherent in application of commonly used technologies to infer analysis of gene expression.
The Value of Serious Play

Two eight-year old children are building a shopping mall with Legos on a Saturday afternoon. One is working on the entrance way and the other is working on two of the mall stores. As the model gets more elaborate, they see that they will soon run out of blocks if they wish to build the mall according to their grand design. They decide to change their strategy and build instead just the entrance way, but with doorways to the stores. They decide they can later use some old shoe boxes for the stores. They tear apart the stores already built and begin building the mall’s entrance way collaboratively with renewed vigor. They even go and get some small house plants and put them in the middle as “trees. ” They continue working for the rest of the afternoon and into the early evening. The mother of one of the children calls to say it’s time to come home for dinner. A bit aggravated by this interruption, the friend agrees to come back tomorrow to help finish the model.
Impact of stroke co-morbidities on cortical collateral flow following ischaemic stroke

Acute hyperglycaemia and chronic hypertension worsen stroke outcome but their impact on collateral perfusion, a determinant of penumbral life span, is poorly understood. Laser-speckle contrast imaging (LSCI) was used to determine the influence of these stroke comorbidities on cortical perfusion after permanent middle cerebral artery occlusion (pMCAO) in spontaneously hypertensive stroke prone rats (SHRSP) and normotensive Wistar rats. Four independent studies were conducted. In animals without pMCAO, cortical perfusion remained stable over 180 min. Following pMCAO, cortical perfusion was markedly reduced at 30 min then gradually increased, via cortical collaterals, over the subsequent 3.5 h. In the contralateral non-ischaemic hemisphere, perfusion did not change over time. Acute hyperglycaemia (in normotensive Wistar) and chronic hypertension (SHRSP) attenuated the restoration of cortical perfusion after pMCAO. Inhaled nitric oxide did not influence cortical perfusion in SHRSP following pMCAO. Thus, hyperglycaemia at the time of arterial occlusion or pre-existing hypertension impaired the dynamic recruitment of cortical collaterals after pMCAO. The impairment of collateral recruitment may contribute to the detrimental effects these comorbidities have on stroke outcome.
The Utility of Skeletal and Surgical Features for the Personal Identification Process: A Pilot Study

This pilot study provides a conceptual framework for the application of the anthropological analysis of skeletal features and surgical interventions for the purpose of identification in cases of unknown deceased individuals with unavailable fingerprint, genetic or odontological antemortem data. The study sample includes 276 individuals with known demographic and clinical information from the Italian CAL Milano Cemetery Skeletal Collection. In the sample, 124 (45%) individuals showed one or more skeletal features that may be potentially individualizing. Of these, 79% showed two and more features, which occurred in a multitude of different combinations. Skeletal findings may provide useful postmortem information that can be compared with antemortem witness statements and clinical imaging. However, more research into the utility of dry bone findings and the availability of comparative material, including imaging, and epidemiological data needs to be undertaken before skeletal features can be implemented into identification protocols and databases.
Finding a Place for Pharmacogenetics in the Electronic Health Record

Many healthcare systems desire to enter the precision medicine era, and pharmacogenetics is seen as a popular first step. However, providers and information technology (IT) staff struggle to keep up with the evolving clinical knowledge and are challenged to incorporate it into the existing workflow of busy providers. To make effective use in the electronic health record (EHR), new approaches must be considered. Leveraging new and evolving standards to make the EHR an open platform is one such approach.
DelPhi Suite: New Developments and Review of Functionalities

Electrostatic potential, energies, and forces affect virtually any process in molecular biology, however, computing these quantities is a difficult task due to irregularly shaped macromolecules and the presence of water. Here, we report a new edition of the popular software package DelPhi along with describing its functionalities. The new DelPhi is a C++ object‐oriented package supporting various levels of multiprocessing and memory distribution. It is demonstrated that multiprocessing results in significant improvement of computational time. Furthermore, for computations requiring large grid size (large macromolecular assemblages), the approach of memory distribution is shown to reduce the requirement of RAM and thus permitting large‐scale modeling to be done on Linux clusters with moderate architecture. The new release comes with new features, whose functionalities and applications are described as well. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
Systemic chemotherapy and survival in patients with metastatic low‐grade appendiceal mucinous adenocarcinoma

Appendiceal cancer is a rare malignancy that exhibits a wide range of histology and treatment response. Given the rarity and heterogeneous nature of the disease, it has been difficult to define optimal treatment strategies. Our goal is to examine the association between use of systemic chemotherapy and survival in patients with metastatic low‐grade mucinous appendiceal adenocarcinoma.
Tracking the evolution of CNS remyelinating lesion in mice with neutral red dye

Significance To develop therapeutic strategies that enhance repair processes during central nervous system (CNS) injury, the molecular and cellular changes occurring at the injury site must be determined. However, precisely isolating the injury site, such as lesions in animal models of demyelination, has been difficult. We developed a simple and powerful method to track and analyze changes that occur within the lesion microenvironment over time. We demonstrated that neutral red-labeled lesions could be selectively isolated and processed for detailed analyses of transcripts, proteins, cell populations, and metabolites. The results of our study can be used to identify molecular pathways that promote CNS repair and the development of therapies to modulate neuroinflammation or enhance regeneration in demyelinating disorders such as multiple sclerosis. Animal models of central nervous system (CNS) demyelination, including toxin-induced focal demyelination and immune-mediated demyelination through experimental autoimmune encephalomyelitis (EAE), have provided valuable insights into the mechanisms of neuroinflammation and CNS remyelination. However, the ability to track changes in transcripts, proteins, and metabolites, as well as cellular populations during the evolution of a focal lesion, has remained challenging. Here, we developed a method to label CNS demyelinating lesions by the intraperitoneal injection of a vital dye, neutral red (NR), into mice before killing. We demonstrate that NR-labeled lesions can be easily identified on the intact spinal cord in both lysolecithin- and EAE-mediated demyelination models. Using fluorescence microscopy, we detected NR in activated macrophages/microglia and astrocytes, but not in oligodendrocytes present in lesions. Importantly, we successfully performed RT-qPCR, Western blot, flow cytometry, and mass spectrometry analysis of precisely dissected NR-labeled lesions at 5, 10, and 20 d postlesion (dpl) and found differential changes in transcripts, proteins, cell populations, and metabolites in lesions over the course of remyelination. Therefore, NR administration is a simple and powerful method to track and analyze the detailed molecular, cellular, and metabolic changes that occur within the lesion microenvironment over time following CNS injury. Furthermore, this method can be used to identify molecular and metabolic pathways that regulate neuroinflammation and remyelination and facilitate the development of therapies to promote repair in demyelinating disorders such as multiple sclerosis.
CRISPR/Cas9‐enhanced ssDNA recombineering for Pseudomonas putida

Implementation of single‐stranded DNA (ssDNA) recombineering in Pseudomonas putida has widened the range of genetic manipulations applicable to this biotechnologically relevant bacterium. Yet, the relatively low efficiency of the technology hampers identification of mutated clones lacking conspicuous phenotypes. Fortunately, the use of CRISPR/Cas9 as a device for counterselection of wild‐type sequences helps to overcome this limitation. Merging ssDNA recombineering with CRISPR/Cas9 thus enables a suite of genomic edits with a straightforward approach: a CRISPR plasmid provides the spacer DNA sequence that directs the Cas9 nuclease ribonucleoprotein complex to cleave the genome at the wild‐type sequences that have not undergone the change entered by the mutagenic ssDNA oligonucleotide(s). This protocol describes a complete workflow of the method optimized for P. putida, although it could in principle be applicable to many other pseudomonads. As an example, we show the deletion of the edd gene that encodes one key enzyme that operates the EDEMP cycle for glucose metabolism in P. putida EM42. By combining two incompatible CRISPR plasmids with different antibiotic selection markers, we show that the procedure can be cycled to implement consecutive deletions in the same strain, e.g. deletion of the pyrF gene following that of the edd mutant. This approach adds to the wealth of genetic technologies available for P. putida and strengthens its status as a chassis of choice for a suite of biotechnological applications.
DNAM-1 and the TIGIT/PVRIG/TACTILE Axis: Novel Immune Checkpoints for Natural Killer Cell-Based Cancer Immunotherapy

Natural killer (NK) cells are lymphocytes of the innate immune response characterized by their role in the destruction of tumor cells. Activation of NK cells depend on a fine balance between activating and inhibitory signals mediated by different receptors. In recent years, a family of paired receptors that interact with ligands of the Nectin/Nectin-like (Necl) family has attracted great interest. Two of these ligands, Necl-5 (usually termed CD155 or PVR) and Nectin-2 (CD112), frequently expressed on different types of tumor cells, are recognized by a group of receptors expressed on T and NK cells that exert opposite functions after interacting with their ligands. These receptors include DNAM-1 (CD226), TIGIT, TACTILE (CD96) and the recently described PVRIG. Whereas activation through DNAM-1 after recognition of CD155 or CD112 enhances NK cell-mediated cytotoxicity against a wide range of tumor cells, TIGIT recognition of these ligands exerts an inhibitory effect on NK cells by diminishing IFN-γ production, as well as NK cell-mediated cytotoxicity. PVRIG has also been identified as an inhibitory receptor that recognizes CD112 but not CD155. However, little is known about the role of TACTILE as modulator of immune responses in humans. TACTILE control of tumor growth and metastases has been reported in murine models, and it has been suggested that it negatively regulates the anti-tumor functions mediated by DNAM-1. In NK cells from patients with solid cancer and leukemia, it has been observed a decreased expression of DNAM-1 that may shift the balance in favor to the inhibitory receptors TIGIT or PVRIG, further contributing to the diminished NK cell-mediated cytotoxic capacity observed in these patients. Analysis of DNAM-1, TIGIT, TACTILE and PVRIG on human NK cells from solid cancer or leukemia patients will clarify the role of these receptors in cancer surveillance. Overall, it can be speculated that in cancer patients the TIGIT/PVRIG pathways are upregulated and represent novel targets for checkpoint blockade immunotherapy.